##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.conc.on.pos.dedup.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
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##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
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##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
##contig=<ID=chrX,length=155270560,assembly=hg19>
##contig=<ID=chrY,length=59373566,assembly=hg19>
##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
##SnpEffVersion="SnpEff 3.1b (build 2012-11-14), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh37.68 -c /Users/arq5x/src/other/snpEff_3_1/snpEff.config -i vcf -o vcf rs-exome.all.raw.nobaq.2012-Nov-15.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE|ALLELE_NUM">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	30548	.	T	G	50.09	.	AC=6;AF=0.429;AN=14;BaseQRankSum=0.000;DP=7;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=29.00;MQ0=0;MQRankSum=-0.550;QD=16.70;ReadPosRankSum=0.937;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),EXON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|1),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|1/2||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1
chr1	30860	.	G	C	54.3	.	AC=3;AF=0.058;AN=52;BaseQRankSum=2.815;DP=61;Dels=0.00;FS=2.403;HRun=0;HaplotypeScore=0.6396;InbreedingCoeff=-0.0048;MQ=36.25;MQ0=0;MQRankSum=0.396;QD=13.57;ReadPosRankSum=2.148;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1
chr1	30867	.	CCT	C	49.48	.	AC=6;AF=0.107;AN=56;BaseQRankSum=0.900;DP=65;FS=0.000;HRun=0;HaplotypeScore=12.2055;InbreedingCoeff=-0.1167;MQ=36.09;MQ0=0;MQRankSum=1.148;QD=3.81;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1
chr1	30895	.	T	C	51.79	.	AC=4;AF=0.069;AN=58;BaseQRankSum=-0.230;DP=63;Dels=0.00;FS=11.041;HRun=0;HaplotypeScore=0.2091;InbreedingCoeff=-0.0237;MQ=36.09;MQ0=0;MQRankSum=1.212;QD=3.98;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1
chr1	30923	.	G	T	601.49	.	AC=30;AF=1.000;AN=30;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1858;MQ=35.61;MQ0=0;QD=35.38;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1
chr1	69270	.	A	G	2971.02	.	AC=53;AF=0.946;AN=56;BaseQRankSum=1.675;DP=100;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0340;InbreedingCoeff=0.1553;MQ=31.06;MQ0=0;MQRankSum=-0.742;QD=31.61;ReadPosRankSum=-1.925;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S60|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=synonymous_variant|tcA/tcG|S|ENSG00000186092|OR4F5|ENST00000335137|1/1|||60/305|protein_coding|1
chr1	69428	.	T	G	938.56	.	AC=3;AF=0.0283;AN=106;BaseQRankSum=-0.638;DP=5013;DS;Dels=0.00;FS=2.607;HRun=0;HaplotypeScore=2.5603;InbreedingCoeff=0.3557;MQ=29.79;MQ0=0;MQRankSum=-5.524;QD=18.40;ReadPosRankSum=4.047;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F113C|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|tTt/tGt|F/C|ENSG00000186092|OR4F5|ENST00000335137|1/1|possibly_damaging(0.568)|deleterious(0)|113/305|protein_coding|1
chr1	69511	.	A	G	101944.44	.	AC=79;AF=0.878;AN=90;BaseQRankSum=-1.592;DP=3853;DS;Dels=0.00;FS=20.586;HRun=0;HaplotypeScore=3.0494;InbreedingCoeff=0.1357;MQ=33.24;MQ0=0;MQRankSum=-12.858;QD=26.51;ReadPosRankSum=-1.756;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|Aca/Gca|T/A|ENSG00000186092|OR4F5|ENST00000335137|1/1|benign(0.003)|tolerated(0.63)|141/305|protein_coding|1
chr1	69761	.	A	T	1026.71	.	AC=8;AF=0.091;AN=88;BaseQRankSum=1.333;DP=574;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3806;InbreedingCoeff=0.5887;MQ=32.18;MQ0=0;MQRankSum=-2.342;QD=21.39;ReadPosRankSum=-3.271;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D224V|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|gAt/gTt|D/V|ENSG00000186092|OR4F5|ENST00000335137|1/1|benign(0.072)|tolerated(0.1)|224/305|protein_coding|1
chr1	69871	.	G	A	82.97	.	AC=2;AF=0.025;AN=80;BaseQRankSum=-0.646;DP=154;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1095;InbreedingCoeff=0.1693;MQ=31.10;MQ0=0;MQRankSum=-0.154;QD=20.74;ReadPosRankSum=-0.292;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D261N|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|Gat/Aat|D/N|ENSG00000186092|OR4F5|ENST00000335137|1/1|probably_damaging(0.968)|tolerated(0.06)|261/305|protein_coding|1
chr1	69897	.	T	C	2544.15	.	AC=52;AF=0.813;AN=64;BaseQRankSum=-0.912;DP=92;Dels=0.00;FS=58.362;HRun=1;HaplotypeScore=0.1549;InbreedingCoeff=0.0561;MQ=30.68;MQ0=0;MQRankSum=3.326;QD=28.59;ReadPosRankSum=1.059;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S269|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=synonymous_variant|tcT/tcC|S|ENSG00000186092|OR4F5|ENST00000335137|1/1|||269/305|protein_coding|1
chr1	861008	.	G	C	1110.54	.	AC=40;AF=0.870;AN=46;BaseQRankSum=1.889;DP=38;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1855;MQ=56.89;MQ0=0;MQRankSum=1.660;QD=33.65;ReadPosRankSum=-1.946;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|1),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|1),UPSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000223764|RP11-54O7.3|ENST00000609207|||||retained_intron|1
chr1	861605	.	C	T	52.33	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.110;DP=330;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2194;InbreedingCoeff=-0.0688;MQ=57.00;MQ0=0;MQRankSum=-0.597;QD=10.47;ReadPosRankSum=-1.210;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	861630	.	G	A	5677.14	.	AC=75;AF=0.7212;AN=104;BaseQRankSum=-3.827;DP=239;Dels=0.00;FS=4.448;HRun=0;HaplotypeScore=0.6050;InbreedingCoeff=0.2720;MQ=57.64;MQ0=0;MQRankSum=-2.334;QD=28.82;ReadPosRankSum=-1.755;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	861808	.	A	G	1231.98	.	AC=34;AF=1.000;AN=34;DP=36;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0587;InbreedingCoeff=-0.1349;MQ=57.39;MQ0=0;QD=34.22;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	864938	.	G	A	38.62	.	AC=4;AF=0.67;AN=6;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=4.771;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=19.31;ReadPosRankSum=0.736;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	865219	.	G	A	271.52	.	AC=14;AF=0.226;AN=62;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=1.303;HRun=0;HaplotypeScore=0.1417;InbreedingCoeff=0.1395;MQ=57.84;MQ0=0;MQRankSum=0.625;QD=14.29;ReadPosRankSum=-0.407;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	865367	.	G	T	48.93	.	AC=2;AF=0.022;AN=90;BaseQRankSum=-0.637;DP=186;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3749;InbreedingCoeff=0.1476;MQ=55.90;MQ0=0;MQRankSum=2.051;QD=16.31;ReadPosRankSum=0.013;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	865435	.	C	G	566.25	.	AC=2;AF=0.0185;AN=108;BaseQRankSum=1.312;DP=479;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6697;InbreedingCoeff=-0.0645;MQ=56.23;MQ0=0;MQRankSum=-0.467;QD=18.88;ReadPosRankSum=-0.530;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	865694	.	C	T	2783.07	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.642;DP=2811;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.6308;InbreedingCoeff=-0.0276;MQ=58.79;MQ0=0;MQRankSum=1.333;QD=13.71;ReadPosRankSum=0.518;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|108|SAMD11|protein_coding|CODING|ENST00000437963|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|178|SAMD11|protein_coding|CODING|ENST00000420190|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000420190|3/7|possibly_damaging(0.493)|tolerated(0.09)|78/179|protein_coding|1,missense_variant|tGc/tAc|C/Y|ENSG00000268179|AL645608.1|ENST00000598827|3/6|possibly_damaging(0.598)||18/112|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000437963|3/5|possibly_damaging(0.493)|tolerated(0.12)|78/109|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000342066|3/14|possibly_damaging(0.493)|tolerated(0.07)|78/681|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000341065|1/12|probably_damaging(0.986)|deleterious(0)|2/589|protein_coding|1
chr1	865738	.	A	G	389.63	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.098;DP=2190;Dels=0.00;FS=12.943;HRun=2;HaplotypeScore=1.1793;InbreedingCoeff=-0.0108;MQ=58.92;MQ0=0;MQRankSum=1.104;QD=9.28;ReadPosRankSum=0.259;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|3),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|3),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|3);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866319	.	G	A	53469.99	.	AC=118;AF=0.9833;AN=120;BaseQRankSum=1.591;DP=1731;Dels=0.00;FS=7.888;HRun=0;HaplotypeScore=1.0922;InbreedingCoeff=-0.0237;MQ=56.60;MQ0=0;MQRankSum=0.921;QD=30.89;ReadPosRankSum=-0.721;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|3),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|3),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|3);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866511	.	C	CCCCT	58244.04	.	AC=74;AF=0.6167;AN=120;BaseQRankSum=-16.318;DP=2662;FS=36.325;HRun=0;HaplotypeScore=234.1454;InbreedingCoeff=-0.0915;MQ=48.89;MQ0=0;MQRankSum=-26.717;QD=25.31;ReadPosRankSum=-3.550;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866515	.	T	TCCCC	28452.17	.	AC=52;AF=0.4333;AN=120;BaseQRankSum=20.767;DP=2538;FS=131.119;HRun=4;HaplotypeScore=272.7313;InbreedingCoeff=-0.6682;MQ=48.42;MQ0=0;MQRankSum=-29.484;QD=13.08;ReadPosRankSum=13.879;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866517	.	C	G	804.92	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.085;DP=2503;Dels=0.00;FS=17.839;HRun=0;HaplotypeScore=16.1376;InbreedingCoeff=-0.0112;MQ=48.27;MQ0=0;MQRankSum=7.710;QD=18.29;ReadPosRankSum=2.729;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866527	.	A	T	4017.89	.	AC=45;AF=0.3750;AN=120;BaseQRankSum=11.973;DP=2186;Dels=0.00;FS=0.676;HRun=0;HaplotypeScore=3.9960;InbreedingCoeff=-0.5937;MQ=46.89;MQ0=0;MQRankSum=0.035;QD=2.40;ReadPosRankSum=-21.689;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866557	.	C	T	127.71	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.174;DP=1561;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7669;InbreedingCoeff=-0.0117;MQ=49.50;MQ0=0;MQRankSum=3.050;QD=5.55;ReadPosRankSum=-0.277;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866731	.	G	C	56.38	.	AC=1;AF=0.011;AN=90;BaseQRankSum=-0.423;DP=139;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1598;InbreedingCoeff=-0.1061;MQ=53.72;MQ0=0;MQRankSum=0.762;QD=14.09;ReadPosRankSum=-0.131;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866893	.	T	C	622.24	.	AC=22;AF=0.500;AN=44;BaseQRankSum=-3.378;DP=42;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0452;InbreedingCoeff=0.1880;MQ=58.67;MQ0=0;MQRankSum=1.917;QD=23.93;ReadPosRankSum=-1.917;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866920	.	A	G	1246.22	.	AC=38;AF=1.000;AN=38;DP=41;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0415;InbreedingCoeff=-0.1594;MQ=58.06;MQ0=0;QD=32.80;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	866938	.	G	A	218.0	.	AC=10;AF=0.278;AN=36;BaseQRankSum=1.425;DP=38;Dels=0.00;FS=4.047;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1861;MQ=59.15;MQ0=0;MQRankSum=0.256;QD=18.17;ReadPosRankSum=-1.863;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	870645	.	T	C	290.54	.	AC=16;AF=0.320;AN=50;BaseQRankSum=-0.425;DP=42;Dels=0.00;FS=3.173;HRun=0;HaplotypeScore=0.0800;InbreedingCoeff=0.0985;MQ=58.33;MQ0=0;MQRankSum=0.337;QD=13.21;ReadPosRankSum=1.918;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	870659	.	G	T	39.74	.	AC=2;AF=0.040;AN=50;BaseQRankSum=1.431;DP=38;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0399;InbreedingCoeff=-0.0066;MQ=57.53;MQ0=0;MQRankSum=0.000;QD=13.25;ReadPosRankSum=1.202;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	870903	.	T	C	4527.15	.	AC=105;AF=0.9722;AN=108;BaseQRankSum=-1.547;DP=151;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=0.3492;InbreedingCoeff=-0.0281;MQ=55.90;MQ0=0;MQRankSum=-1.281;QD=30.59;ReadPosRankSum=-1.215;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871020	.	G	A	123.6	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.361;DP=922;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6728;InbreedingCoeff=-0.0124;MQ=58.46;MQ0=0;MQRankSum=0.878;QD=12.36;ReadPosRankSum=0.658;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871042	.	C	CA	1121.53	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.932;DP=1196;FS=4.192;HRun=1;HaplotypeScore=68.0502;InbreedingCoeff=-0.0178;MQ=58.64;MQ0=0;MQRankSum=0.039;QD=20.77;ReadPosRankSum=1.478;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871215	.	C	G	3347.1	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.247;DP=4311;Dels=0.00;FS=7.397;HRun=1;HaplotypeScore=1.9160;InbreedingCoeff=-0.0257;MQ=58.16;MQ0=0;MQRankSum=2.137;QD=13.44;ReadPosRankSum=0.832;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P123|178|SAMD11|protein_coding|CODING|ENST00000420190|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P123|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000420190|5/7|||123/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000342066|5/14|||123/681|protein_coding|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000341065|3/12|||47/589|protein_coding|1
chr1	871306	.	G	A	333.26	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.027;DP=2068;Dels=0.00;FS=3.159;HRun=0;HaplotypeScore=2.0683;InbreedingCoeff=-0.0097;MQ=57.05;MQ0=0;MQRankSum=0.683;QD=9.52;ReadPosRankSum=0.829;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871334	.	G	T	28303.7	.	AC=78;AF=0.6500;AN=120;BaseQRankSum=-4.675;DP=1477;Dels=0.00;FS=1.219;HRun=0;HaplotypeScore=0.8602;InbreedingCoeff=-0.1122;MQ=57.60;MQ0=0;MQRankSum=3.104;QD=21.15;ReadPosRankSum=-0.389;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871406	.	C	T	373.38	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.644;DP=663;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3801;InbreedingCoeff=-0.0188;MQ=58.43;MQ0=0;MQRankSum=0.382;QD=14.94;ReadPosRankSum=0.041;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	871513	.	C	T	90.88	.	AC=2;AF=0.0196;AN=102;BaseQRankSum=0.045;DP=143;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1691;InbreedingCoeff=0.0569;MQ=57.57;MQ0=0;MQRankSum=-0.474;QD=22.72;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1
chr1	871683	.	G	A	69.81	.	AC=6;AF=0.375;AN=16;BaseQRankSum=0.684;DP=8;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2498;MQ=58.46;MQ0=0;MQRankSum=1.221;QD=23.27;ReadPosRankSum=0.684;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1
chr1	874314	.	G	A	306.48	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.210;DP=904;Dels=0.00;FS=2.007;HRun=2;HaplotypeScore=0.6052;InbreedingCoeff=-0.0150;MQ=58.05;MQ0=0;MQRankSum=-1.582;QD=10.95;ReadPosRankSum=0.649;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874415	.	C	T	459.1	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.071;DP=2210;Dels=0.00;FS=0.832;HRun=0;HaplotypeScore=1.8123;InbreedingCoeff=-0.0101;MQ=58.23;MQ0=0;MQRankSum=1.495;QD=12.08;ReadPosRankSum=0.643;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874665	.	G	A	1190.84	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.904;DP=2083;Dels=0.00;FS=5.872;HRun=0;HaplotypeScore=1.2968;InbreedingCoeff=-0.0278;MQ=57.54;MQ0=0;MQRankSum=1.122;QD=14.35;ReadPosRankSum=0.856;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L177|178|SAMD11|protein_coding|CODING|ENST00000420190|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L177|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000420190|7/7|||177/179|protein_coding|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000342066|7/14|||177/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000455979|1/7|||4/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000341065|5/12|||101/589|protein_coding|1
chr1	874816	.	C	CT	2431.73	.	AC=13;AF=0.1083;AN=120;BaseQRankSum=-3.645;DP=2129;FS=0.000;HRun=1;HaplotypeScore=136.3097;InbreedingCoeff=0.2233;MQ=55.95;MQ0=0;MQRankSum=-0.937;QD=9.11;ReadPosRankSum=-4.095;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),FRAME_SHIFT(HIGH||-/T|-228?|681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,frameshift_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066|7/14|||228/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,frameshift_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979|1/7|||55/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874817	.	C	T	196.11	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-3.463;DP=2129;Dels=0.00;FS=3.213;HRun=0;HaplotypeScore=3.1349;InbreedingCoeff=-0.0440;MQ=55.95;MQ0=0;MQRankSum=1.345;QD=2.84;ReadPosRankSum=-3.888;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P228L|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|cCc/cTc|P/L|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0.003)|tolerated(0.26)|228/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|cCc/cTc|P/L|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0.086)|tolerated(0.06)|55/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874825	.	C	G	56.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.967;DP=2039;Dels=0.00;FS=3.631;HRun=0;HaplotypeScore=3.2093;InbreedingCoeff=-0.0100;MQ=55.77;MQ0=0;MQRankSum=0.586;QD=4.71;ReadPosRankSum=-3.947;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H231D|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|Cac/Gac|H/D|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0)|tolerated(0.23)|231/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|Cac/Gac|H/D|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0.001)|tolerated(0.22)|58/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874826	.	A	G	43.49	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.114;DP=2017;Dels=0.00;FS=12.409;HRun=0;HaplotypeScore=2.9313;InbreedingCoeff=-0.0145;MQ=55.77;MQ0=0;MQRankSum=1.636;QD=3.62;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H231R|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|cAc/cGc|H/R|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0)|tolerated(0.37)|231/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|cAc/cGc|H/R|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0)|tolerated(0.36)|58/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874864	.	CT	C	864.62	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=2.646;DP=1615;FS=13.206;HRun=1;HaplotypeScore=111.2623;InbreedingCoeff=-0.0402;MQ=54.48;MQ0=0;MQRankSum=-2.660;QD=5.84;ReadPosRankSum=-2.656;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874878	.	T	C	30.73	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-11.417;DP=1417;Dels=0.00;FS=9.439;HRun=4;HaplotypeScore=1.6844;InbreedingCoeff=-0.0402;MQ=53.55;MQ0=0;MQRankSum=0.037;QD=0.29;ReadPosRankSum=-3.513;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874927	.	A	G	459.72	.	AC=5;AF=0.0439;AN=114;BaseQRankSum=2.529;DP=728;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5050;InbreedingCoeff=0.1366;MQ=49.13;MQ0=0;MQRankSum=-1.720;QD=7.93;ReadPosRankSum=0.425;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874933	.	G	A	71.83	.	AC=2;AF=0.0175;AN=114;BaseQRankSum=-2.598;DP=677;Dels=0.00;FS=12.021;HRun=0;HaplotypeScore=0.5171;InbreedingCoeff=0.3582;MQ=48.55;MQ0=0;MQRankSum=-2.054;QD=17.96;ReadPosRankSum=-0.568;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874949	.	G	GAC	180.07	.	AC=12;AF=0.1091;AN=110;BaseQRankSum=4.227;DP=513;FS=1.980;HRun=0;HaplotypeScore=80.8744;InbreedingCoeff=-0.1326;MQ=45.53;MQ0=0;MQRankSum=0.812;QD=1.55;ReadPosRankSum=-6.278;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874950	.	T	C	171.91	.	AC=11;AF=0.1000;AN=110;BaseQRankSum=-0.909;DP=513;Dels=0.00;FS=2.116;HRun=3;HaplotypeScore=3.7881;InbreedingCoeff=-0.1427;MQ=45.53;MQ0=0;MQRankSum=5.553;QD=1.55;ReadPosRankSum=-4.349;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874950	.	T	TCCCTGGAGGACC	52769.69	.	AC=82;AF=0.7455;AN=110;BaseQRankSum=-5.074;DP=556;FS=0.992;HRun=0;HaplotypeScore=89.5226;InbreedingCoeff=-0.2281;MQ=43.74;MQ0=0;MQRankSum=-13.823;QD=95.42;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	874955	.	C	G	162.26	.	AC=15;AF=0.1364;AN=110;BaseQRankSum=-1.052;DP=411;Dels=0.00;FS=15.434;HRun=0;HaplotypeScore=3.6422;InbreedingCoeff=-0.1058;MQ=46.15;MQ0=0;MQRankSum=4.641;QD=1.62;ReadPosRankSum=-7.007;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	875159	.	AGCCAGTGGACGCCGACCT	A	727.04	.	AC=15;AF=0.500;AN=30;BaseQRankSum=3.932;DP=27;FS=0.000;HRun=0;HaplotypeScore=24.4581;InbreedingCoeff=0.3261;MQ=51.25;MQ0=0;MQRankSum=-2.825;QD=80.78;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	876498	.	GA	G	1427.8	.	AC=48;AF=0.4000;AN=120;BaseQRankSum=-5.371;DP=794;FS=21.973;HRun=1;HaplotypeScore=83.2253;InbreedingCoeff=-0.3157;MQ=58.06;MQ0=0;MQRankSum=0.970;QD=2.48;ReadPosRankSum=-12.769;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	876499	.	A	G	22430.37	.	AC=114;AF=0.9500;AN=120;BaseQRankSum=2.512;DP=794;Dels=0.01;FS=0.566;HRun=6;HaplotypeScore=0.6449;InbreedingCoeff=-0.0691;MQ=58.06;MQ0=0;MQRankSum=0.580;QD=28.25;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	876595	.	C	T	278.95	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.357;DP=1272;Dels=0.00;FS=1.349;HRun=0;HaplotypeScore=0.7550;InbreedingCoeff=-0.0197;MQ=57.15;MQ0=0;MQRankSum=0.060;QD=13.28;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P260S|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000342066|8/14|probably_damaging(0.987)|deleterious(0)|260/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000455979|2/7|probably_damaging(0.999)|deleterious(0)|87/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|2/3||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000341065|6/12|probably_damaging(0.999)|tolerated(0.05)|168/589|protein_coding|1
chr1	876908	.	G	A	134.68	.	AC=1;AF=0.013;AN=80;BaseQRankSum=1.386;DP=184;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2023;InbreedingCoeff=-0.0861;MQ=56.39;MQ0=0;MQRankSum=0.341;QD=14.96;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|8),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	877147	.	G	A	43.79	.	AC=6;AF=0.273;AN=22;BaseQRankSum=-0.925;DP=17;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.2867;MQ=52.81;MQ0=0;MQRankSum=0.185;QD=14.60;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|8),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	877715	.	C	G	5039.18	.	AC=98;AF=0.9423;AN=104;BaseQRankSum=1.292;DP=191;Dels=0.00;FS=2.185;HRun=3;HaplotypeScore=0.2807;InbreedingCoeff=-0.0534;MQ=53.91;MQ0=0;MQRankSum=-0.346;QD=26.66;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|9),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|1),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|2);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	877782	.	C	G	59.43	.	AC=4;AF=0.0357;AN=112;BaseQRankSum=-0.568;DP=212;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0665;InbreedingCoeff=0.0350;MQ=54.31;MQ0=0;MQRankSum=1.437;QD=5.40;ReadPosRankSum=0.130;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|9),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|1),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|2);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	877831	.	T	C	5022.11	.	AC=102;AF=1.0000;AN=102;BaseQRankSum=1.709;DP=173;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.1329;InbreedingCoeff=-0.0991;MQ=53.24;MQ0=0;MQRankSum=1.638;QD=29.20;ReadPosRankSum=-0.772;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|2),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W343R|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000342066|10/14|benign(0)|tolerated(1)|343/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|2/2||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|3/4||||retained_intron|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000455979|4/7|benign(0)|tolerated(1)|170/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000341065|8/12|benign(0)|tolerated(1)|251/589|protein_coding|1
chr1	878314	.	G	C	762.28	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=0.711;DP=450;Dels=0.00;FS=2.520;HRun=0;HaplotypeScore=0.3685;InbreedingCoeff=-0.1321;MQ=57.76;MQ0=0;MQRankSum=1.717;QD=9.30;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|4),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G480|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000342066|11/14|||480/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|4/4||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000455979|5/7|||307/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000341065|9/12|||388/589|protein_coding|1
chr1	878331	.	C	T	170.27	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.516;DP=507;Dels=0.00;FS=13.852;HRun=0;HaplotypeScore=0.4065;InbreedingCoeff=-0.0252;MQ=57.83;MQ0=0;MQRankSum=0.921;QD=21.28;ReadPosRankSum=-1.361;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|4),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P486L|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000342066|11/14|benign(0.007)|tolerated(0.12)|486/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|4/4||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000455979|5/7|benign(0.029)|tolerated(0.09)|313/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000341065|9/12|benign(0.006)|tolerated(0.18)|394/589|protein_coding|1
chr1	878516	.	GA	G	725.28	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=4.091;DP=1587;FS=6.039;HRun=5;HaplotypeScore=109.1933;InbreedingCoeff=-0.0395;MQ=57.40;MQ0=0;MQRankSum=0.773;QD=10.67;ReadPosRankSum=1.454;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|11);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	878761	.	A	AG	102.98	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.641;DP=955;FS=3.593;HRun=7;HaplotypeScore=63.6389;InbreedingCoeff=-0.0174;MQ=56.57;MQ0=0;MQRankSum=0.356;QD=4.90;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	878764	.	G	C	139.53	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.470;DP=938;Dels=0.00;FS=7.307;HRun=0;HaplotypeScore=0.9091;InbreedingCoeff=-0.0119;MQ=56.61;MQ0=0;MQRankSum=1.683;QD=9.97;ReadPosRankSum=2.283;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	878904	.	A	C	629.76	.	AC=27;AF=0.270;AN=100;BaseQRankSum=-10.394;DP=328;Dels=0.01;FS=66.455;HRun=4;HaplotypeScore=5.0793;InbreedingCoeff=-0.3279;MQ=45.67;MQ0=0;MQRankSum=-7.168;QD=2.59;ReadPosRankSum=7.847;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	878906	.	CTTT	C	498.81	.	AC=35;AF=0.407;AN=86;BaseQRankSum=-0.896;DP=307;FS=10.838;HRun=22;HaplotypeScore=48.3314;InbreedingCoeff=0.1154;MQ=44.42;MQ0=0;MQRankSum=-1.401;QD=2.60;ReadPosRankSum=2.748;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	879195	.	C	T	744.73	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.733;DP=2228;Dels=0.00;FS=2.345;HRun=0;HaplotypeScore=2.3431;InbreedingCoeff=-0.0106;MQ=57.41;MQ0=0;MQRankSum=1.176;QD=11.82;ReadPosRankSum=0.278;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|13);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,missense_variant|Cgc/Tgc|R/C|ENSG00000187634|SAMD11|ENST00000455979|7/7|benign(0.047)|tolerated(0.15)|430/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	879317	.	C	T	1801.69	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=0.490;DP=1511;Dels=0.00;FS=0.480;HRun=0;HaplotypeScore=0.8559;InbreedingCoeff=-0.0439;MQ=57.96;MQ0=0;MQRankSum=-0.001;QD=13.15;ReadPosRankSum=0.731;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y610|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000342066|14/14|||610/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000455979|7/7|||470/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000341065|12/12|||518/589|protein_coding|1
chr1	879376	.	G	A	35.51	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.159;DP=1323;Dels=0.00;FS=4.217;HRun=1;HaplotypeScore=0.6368;InbreedingCoeff=-0.0128;MQ=58.52;MQ0=0;MQRankSum=2.465;QD=2.96;ReadPosRankSum=0.209;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R630Q|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000342066|14/14|benign(0.048)|tolerated(0.13)|630/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000455979|7/7|benign(0.024)|tolerated(0.19)|490/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000341065|12/12|benign(0.012)|tolerated(0.16)|538/589|protein_coding|1
chr1	879482	.	G	C	516.68	.	AC=1;AF=0.0088;AN=114;BaseQRankSum=2.415;DP=1065;Dels=0.00;FS=3.604;HRun=0;HaplotypeScore=0.8043;InbreedingCoeff=-0.0358;MQ=59.14;MQ0=0;MQRankSum=0.854;QD=17.82;ReadPosRankSum=-1.823;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G665|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000342066|14/14|||665/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000455979|7/7|||525/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000341065|12/12|||573/589|protein_coding|1
chr1	879676	.	G	A	6945.69	.	AC=71;AF=0.934;AN=76;BaseQRankSum=-1.592;DP=208;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0908;InbreedingCoeff=0.0037;MQ=56.70;MQ0=0;MQRankSum=-0.599;QD=33.55;ReadPosRankSum=-1.965;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1
chr1	879687	.	T	C	5518.2	.	AC=65;AF=0.956;AN=68;BaseQRankSum=0.725;DP=166;Dels=0.00;FS=1.578;HRun=1;HaplotypeScore=0.1048;InbreedingCoeff=0.0533;MQ=56.43;MQ0=0;MQRankSum=0.068;QD=33.44;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1
chr1	879911	.	G	A	413.77	.	AC=3;AF=0.0254;AN=118;BaseQRankSum=-0.760;DP=308;Dels=0.00;FS=1.528;HRun=1;HaplotypeScore=0.1788;InbreedingCoeff=-0.0710;MQ=57.83;MQ0=0;MQRankSum=0.760;QD=15.32;ReadPosRankSum=0.384;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1
chr1	880110	.	G	A	149.9	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.394;DP=1847;Dels=0.00;FS=1.624;HRun=0;HaplotypeScore=0.9203;InbreedingCoeff=-0.0094;MQ=57.47;MQ0=0;MQRankSum=1.220;QD=6.25;ReadPosRankSum=0.988;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D738|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000188976|NOC2L|ENST00000327044|19/19|||738/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880238	.	A	G	43084.12	.	AC=114;AF=0.9500;AN=120;BaseQRankSum=-0.613;DP=1203;Dels=0.00;FS=12.344;HRun=1;HaplotypeScore=1.0677;InbreedingCoeff=-0.0525;MQ=58.52;MQ0=0;MQRankSum=-1.859;QD=35.81;ReadPosRankSum=-0.535;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880258	.	TAA	T	1233.06	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.890;DP=1382;FS=2.604;HRun=2;HaplotypeScore=131.0286;InbreedingCoeff=-0.0085;MQ=58.89;MQ0=0;MQRankSum=1.259;QD=20.55;ReadPosRankSum=-3.041;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880367	.	G	A	795.59	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.447;DP=3095;Dels=0.00;FS=7.414;HRun=0;HaplotypeScore=2.5302;InbreedingCoeff=-0.0084;MQ=58.79;MQ0=0;MQRankSum=0.556;QD=10.61;ReadPosRankSum=0.729;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880390	.	C	A	4207.41	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-1.360;DP=3838;Dels=0.00;FS=18.983;HRun=0;HaplotypeScore=2.5364;InbreedingCoeff=-0.0345;MQ=58.94;MQ0=0;MQRankSum=0.010;QD=14.76;ReadPosRankSum=1.464;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880483	.	A	G	739.51	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.408;DP=5022;DS;Dels=0.00;FS=13.337;HRun=0;HaplotypeScore=2.6561;InbreedingCoeff=-0.0170;MQ=59.08;MQ0=0;MQRankSum=0.004;QD=12.75;ReadPosRankSum=-2.856;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D699|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000188976|NOC2L|ENST00000327044|18/19|||699/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|4/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|16/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880639	.	TC	T	8144.14	.	AC=31;AF=0.2583;AN=120;BaseQRankSum=8.550;DP=921;FS=0.348;HRun=2;HaplotypeScore=54.1306;InbreedingCoeff=-0.1017;MQ=58.66;MQ0=0;MQRankSum=1.840;QD=17.70;ReadPosRankSum=1.996;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|17),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	880751	.	A	G	807.9	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=1.558;DP=1112;Dels=0.00;FS=1.129;HRun=1;HaplotypeScore=0.7010;InbreedingCoeff=0.4309;MQ=58.97;MQ0=0;MQRankSum=3.000;QD=18.79;ReadPosRankSum=0.469;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|2),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|17),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000496938|2/2||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881027	.	C	G	2780.96	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.239;DP=6197;DS;Dels=0.00;FS=8.993;HRun=0;HaplotypeScore=3.1641;InbreedingCoeff=-0.0084;MQ=59.26;MQ0=0;MQRankSum=2.376;QD=14.56;ReadPosRankSum=-0.209;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Cac|D642H|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|Gac/Cac|D/H|ENSG00000188976|NOC2L|ENST00000327044|17/19|probably_damaging(0.928)|deleterious(0)|642/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|3/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|15/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881068	.	G	A	311.66	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.528;DP=3714;DS;Dels=0.00;FS=2.094;HRun=1;HaplotypeScore=2.7083;InbreedingCoeff=-0.0084;MQ=58.85;MQ0=0;MQRankSum=2.312;QD=14.17;ReadPosRankSum=-1.657;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881214	.	A	G	121.77	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.359;DP=622;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2865;InbreedingCoeff=-0.0200;MQ=58.09;MQ0=0;MQRankSum=-1.890;QD=15.22;ReadPosRankSum=-1.501;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881278	.	T	C	73.18	.	AC=5;AF=0.0472;AN=106;BaseQRankSum=-5.288;DP=225;Dels=0.00;FS=14.303;HRun=2;HaplotypeScore=0.2150;InbreedingCoeff=-0.1298;MQ=55.77;MQ0=0;MQRankSum=-0.007;QD=2.36;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881377	.	G	A	198.25	.	AC=3;AF=0.0259;AN=116;BaseQRankSum=0.943;DP=299;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1931;InbreedingCoeff=-0.0772;MQ=57.25;MQ0=0;MQRankSum=1.239;QD=11.01;ReadPosRankSum=1.934;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881512	.	G	T	329.45	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.087;DP=1882;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4710;InbreedingCoeff=-0.0118;MQ=58.18;MQ0=0;MQRankSum=0.210;QD=11.36;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881627	.	G	A	65058.1	.	AC=69;AF=0.5750;AN=120;BaseQRankSum=-0.436;DP=4175;Dels=0.00;FS=7.028;HRun=1;HaplotypeScore=3.6325;InbreedingCoeff=0.0788;MQ=58.73;MQ0=0;MQRankSum=0.133;QD=20.93;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L615|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|Ctg/Ttg|L|ENSG00000188976|NOC2L|ENST00000327044|16/19|||615/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|2/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|14/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881734	.	T	C	2395.2	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=1.087;DP=3324;Dels=0.00;FS=13.773;HRun=0;HaplotypeScore=2.3394;InbreedingCoeff=-0.0275;MQ=58.22;MQ0=0;MQRankSum=4.896;QD=14.34;ReadPosRankSum=1.344;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881894	.	G	A	502.77	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.087;DP=3111;Dels=0.00;FS=0.806;HRun=0;HaplotypeScore=1.9434;InbreedingCoeff=-0.0084;MQ=55.95;MQ0=0;MQRankSum=4.130;QD=7.62;ReadPosRankSum=-0.465;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A564V|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|gCc/gTc|A/V|ENSG00000188976|NOC2L|ENST00000327044|15/19|probably_damaging(0.911)|deleterious(0)|564/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|13/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	881918	.	G	A	4148.23	.	AC=6;AF=0.0500;AN=120;BaseQRankSum=0.336;DP=2717;Dels=0.00;FS=3.311;HRun=1;HaplotypeScore=1.8603;InbreedingCoeff=-0.0526;MQ=57.50;MQ0=0;MQRankSum=10.868;QD=13.38;ReadPosRankSum=2.821;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S556L|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|tCg/tTg|S/L|ENSG00000188976|NOC2L|ENST00000327044|15/19|benign(0.311)|deleterious(0.03)|556/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|13/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	882033	.	G	A	7803.05	.	AC=29;AF=0.2417;AN=120;BaseQRankSum=-1.083;DP=803;Dels=0.00;FS=0.805;HRun=1;HaplotypeScore=0.5525;InbreedingCoeff=-0.0708;MQ=56.82;MQ0=0;MQRankSum=1.538;QD=18.99;ReadPosRankSum=-1.493;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|12),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	883625	.	A	G	54754.53	.	AC=120;AF=1.0000;AN=120;DP=1639;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.0098;InbreedingCoeff=-0.0052;MQ=58.06;MQ0=0;QD=33.41;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	883699	.	C	T	453.1	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.101;DP=923;Dels=0.00;FS=14.883;HRun=0;HaplotypeScore=0.5131;InbreedingCoeff=-0.0294;MQ=56.96;MQ0=0;MQRankSum=3.137;QD=12.25;ReadPosRankSum=2.276;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	883750	.	T	C	877.5	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=1.693;DP=1077;Dels=0.00;FS=5.318;HRun=3;HaplotypeScore=0.3559;InbreedingCoeff=-0.0265;MQ=57.03;MQ0=0;MQRankSum=4.377;QD=17.21;ReadPosRankSum=1.955;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	883960	.	G	A	483.87	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.195;DP=3321;Dels=0.00;FS=1.899;HRun=0;HaplotypeScore=1.8090;InbreedingCoeff=-0.0084;MQ=57.94;MQ0=0;MQRankSum=2.447;QD=10.30;ReadPosRankSum=1.425;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N489|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|aaC/aaT|N|ENSG00000188976|NOC2L|ENST00000327044|13/19|||489/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|11/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884013	.	G	A	359.69	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.049;DP=1892;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9736;InbreedingCoeff=-0.0084;MQ=57.09;MQ0=0;MQRankSum=2.918;QD=14.99;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884035	.	G	GCC	125.11	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=10.429;DP=1507;FS=5.790;HRun=1;HaplotypeScore=118.1286;InbreedingCoeff=-0.1150;MQ=55.10;MQ0=0;MQRankSum=-9.464;QD=0.53;ReadPosRankSum=-1.582;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884040	.	AC	A	54.58	.	AC=10;AF=0.0833;AN=120;BaseQRankSum=10.370;DP=1485;FS=5.837;HRun=3;HaplotypeScore=105.2143;InbreedingCoeff=-0.0972;MQ=54.77;MQ0=0;MQRankSum=-6.138;QD=0.29;ReadPosRankSum=-3.294;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884091	.	C	G	9412.98	.	AC=59;AF=0.4917;AN=120;BaseQRankSum=0.144;DP=830;Dels=0.00;FS=3.690;HRun=1;HaplotypeScore=1.5824;InbreedingCoeff=-0.8297;MQ=49.85;MQ0=0;MQRankSum=3.025;QD=11.58;ReadPosRankSum=6.853;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884101	.	A	C	9419.59	.	AC=54;AF=0.4500;AN=120;BaseQRankSum=12.324;DP=697;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=1.3334;InbreedingCoeff=-0.7661;MQ=48.44;MQ0=0;MQRankSum=-6.895;QD=14.45;ReadPosRankSum=-14.010;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884111	.	T	C	106.0	.	AC=12;AF=0.1017;AN=118;BaseQRankSum=-1.701;DP=405;Dels=0.00;FS=32.333;HRun=2;HaplotypeScore=0.1962;InbreedingCoeff=-0.1423;MQ=53.01;MQ0=0;MQRankSum=1.879;QD=1.39;ReadPosRankSum=-6.750;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	884426	.	A	AACAGCAAAG	1975.5	.	AC=28;AF=1.000;AN=28;DP=24;FS=0.000;HRun=0;HaplotypeScore=8.5806;InbreedingCoeff=-0.1820;MQ=37.89;MQ0=0;QD=98.77;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1
chr1	886006	.	T	C	1030.61	.	AC=32;AF=1.000;AN=32;DP=31;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1369;MQ=49.82;MQ0=0;QD=33.25;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886049	.	ACAG	A	1495.02	.	AC=34;AF=0.944;AN=36;BaseQRankSum=1.722;DP=33;FS=2.691;HRun=0;HaplotypeScore=10.4318;InbreedingCoeff=0.1010;MQ=41.07;MQ0=0;MQRankSum=-2.098;QD=49.83;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886179	.	CA	C	1612.0	.	AC=47;AF=0.870;AN=54;BaseQRankSum=3.364;DP=49;FS=8.293;HRun=1;HaplotypeScore=18.7687;InbreedingCoeff=0.1732;MQ=36.71;MQ0=0;MQRankSum=-3.123;QD=36.64;ReadPosRankSum=0.259;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886182	.	TG	T	1532.98	.	AC=47;AF=0.870;AN=54;BaseQRankSum=3.246;DP=46;FS=5.278;HRun=1;HaplotypeScore=18.4565;InbreedingCoeff=0.1421;MQ=34.65;MQ0=0;MQRankSum=-2.960;QD=36.50;ReadPosRankSum=0.184;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886186	.	C	CAG	2268.91	.	AC=57;AF=0.891;AN=64;BaseQRankSum=3.232;DP=55;FS=6.052;HRun=0;HaplotypeScore=17.8027;InbreedingCoeff=0.1016;MQ=34.53;MQ0=0;MQRankSum=-3.122;QD=44.49;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886384	.	G	A	434.04	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.231;DP=475;Dels=0.00;FS=8.266;HRun=0;HaplotypeScore=0.2516;InbreedingCoeff=-0.0534;MQ=58.22;MQ0=0;MQRankSum=1.803;QD=11.42;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886409	.	G	C	225.93	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.047;DP=629;Dels=0.00;FS=1.803;HRun=2;HaplotypeScore=0.3393;InbreedingCoeff=-0.0500;MQ=58.47;MQ0=0;MQRankSum=0.500;QD=5.79;ReadPosRankSum=-0.845;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886477	.	G	A	1109.56	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.561;DP=1412;Dels=0.00;FS=5.360;HRun=0;HaplotypeScore=1.3637;InbreedingCoeff=-0.0325;MQ=58.75;MQ0=0;MQRankSum=0.602;QD=11.56;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886492	.	C	T	237.45	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.074;DP=1595;Dels=0.00;FS=5.466;HRun=0;HaplotypeScore=0.8808;InbreedingCoeff=0.7925;MQ=58.78;MQ0=0;MQRankSum=0.397;QD=21.59;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886653	.	G	A	558.63	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=1.368;DP=1520;Dels=0.00;FS=21.500;HRun=0;HaplotypeScore=1.1951;InbreedingCoeff=-0.0285;MQ=58.36;MQ0=0;MQRankSum=0.809;QD=15.52;ReadPosRankSum=-1.905;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886788	.	G	A	9988.89	.	AC=98;AF=0.8305;AN=118;BaseQRankSum=-1.367;DP=334;Dels=0.00;FS=18.012;HRun=1;HaplotypeScore=0.1988;InbreedingCoeff=0.2452;MQ=57.31;MQ0=0;MQRankSum=4.299;QD=32.86;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886817	.	C	T	6332.01	.	AC=90;AF=0.8182;AN=110;BaseQRankSum=-1.237;DP=216;Dels=0.00;FS=12.660;HRun=3;HaplotypeScore=0.3611;InbreedingCoeff=0.1623;MQ=57.12;MQ0=0;MQRankSum=2.897;QD=31.50;ReadPosRankSum=0.605;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	886817	.	C	CATTTT	1195.05	.	AC=14;AF=0.1296;AN=108;BaseQRankSum=-6.408;DP=215;FS=1.303;HRun=0;HaplotypeScore=40.0482;InbreedingCoeff=0.0654;MQ=57.03;MQ0=0;MQRankSum=-3.623;QD=23.43;ReadPosRankSum=-3.297;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887162	.	T	C	158.95	.	AC=3;AF=0.0273;AN=110;BaseQRankSum=0.867;DP=242;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1059;InbreedingCoeff=-0.1008;MQ=57.95;MQ0=0;MQRankSum=1.543;QD=10.60;ReadPosRankSum=-1.064;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887265	.	C	A	101.07	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.874;DP=895;Dels=0.00;FS=2.947;HRun=0;HaplotypeScore=0.4283;InbreedingCoeff=-0.0106;MQ=59.14;MQ0=0;MQRankSum=2.148;QD=6.74;ReadPosRankSum=-0.250;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887471	.	G	A	581.35	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.013;DP=3085;Dels=0.00;FS=3.856;HRun=1;HaplotypeScore=1.5844;InbreedingCoeff=-0.0084;MQ=59.14;MQ0=0;MQRankSum=3.944;QD=12.92;ReadPosRankSum=0.093;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L414|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=synonymous_variant|Ctg/Ttg|L|ENSG00000188976|NOC2L|ENST00000327044|11/19|||414/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|9/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887537	.	C	T	1658.47	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=1.815;DP=2530;Dels=0.00;FS=6.149;HRun=0;HaplotypeScore=1.6593;InbreedingCoeff=-0.0258;MQ=59.28;MQ0=0;MQRankSum=2.238;QD=12.11;ReadPosRankSum=2.057;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887560	.	A	C	70115.69	.	AC=113;AF=0.9417;AN=120;BaseQRankSum=0.848;DP=2150;Dels=0.00;FS=10.744;HRun=1;HaplotypeScore=1.3105;InbreedingCoeff=0.2414;MQ=59.13;MQ0=0;MQRankSum=-0.778;QD=32.87;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887651	.	C	T	665.1	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.019;DP=1257;Dels=0.00;FS=1.751;HRun=0;HaplotypeScore=0.9128;InbreedingCoeff=-0.0177;MQ=58.63;MQ0=0;MQRankSum=3.510;QD=17.50;ReadPosRankSum=2.127;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	887801	.	A	G	116758.48	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=4.615;DP=3778;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=2.1571;InbreedingCoeff=-0.0435;MQ=57.90;MQ0=0;MQRankSum=2.145;QD=30.90;ReadPosRankSum=1.213;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T394|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=synonymous_variant|acT/acC|T|ENSG00000188976|NOC2L|ENST00000327044|10/19|||394/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|8/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	888220	.	G	A	81.05	.	AC=4;AF=0.044;AN=90;BaseQRankSum=-1.159;DP=137;Dels=0.00;FS=2.348;HRun=0;HaplotypeScore=0.1677;InbreedingCoeff=-0.0166;MQ=57.57;MQ0=0;MQRankSum=1.051;QD=7.37;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|9),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	888239	.	C	T	79.33	.	AC=3;AF=0.034;AN=88;BaseQRankSum=0.324;DP=113;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0969;InbreedingCoeff=-0.0212;MQ=57.69;MQ0=0;MQRankSum=1.258;QD=13.22;ReadPosRankSum=-0.910;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|9),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	888639	.	T	C	94387.16	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=0.263;DP=3128;Dels=0.00;FS=2.314;HRun=1;HaplotypeScore=1.2974;InbreedingCoeff=-0.0435;MQ=54.95;MQ0=0;MQRankSum=0.465;QD=30.17;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E306|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,synonymous_variant|gaA/gaG|E|ENSG00000188976|NOC2L|ENST00000327044|9/19|||306/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|7/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	888659	.	T	C	80634.32	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=1.739;DP=2737;Dels=0.00;FS=2.276;HRun=1;HaplotypeScore=1.3379;InbreedingCoeff=-0.0436;MQ=54.78;MQ0=0;MQRankSum=-1.113;QD=29.46;ReadPosRankSum=4.132;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I300V|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,missense_variant|Atc/Gtc|I/V|ENSG00000188976|NOC2L|ENST00000327044|9/19|benign(0)|tolerated(0.98)|300/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|7/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889131	.	A	G	423.54	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.236;DP=1138;Dels=0.00;FS=7.564;HRun=1;HaplotypeScore=0.6841;InbreedingCoeff=-0.0300;MQ=57.89;MQ0=0;MQRankSum=0.858;QD=9.41;ReadPosRankSum=0.777;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889158	.	G	C	40721.48	.	AC=113;AF=0.9417;AN=120;BaseQRankSum=1.359;DP=1345;Dels=0.00;FS=0.512;HRun=1;HaplotypeScore=0.9432;InbreedingCoeff=0.2187;MQ=58.28;MQ0=0;MQRankSum=1.507;QD=30.55;ReadPosRankSum=0.613;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889159	.	A	C	41244.53	.	AC=113;AF=0.9417;AN=120;BaseQRankSum=1.309;DP=1361;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8382;InbreedingCoeff=0.2198;MQ=58.26;MQ0=0;MQRankSum=1.567;QD=30.57;ReadPosRankSum=1.331;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889238	.	G	A	1672.71	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.383;DP=1656;Dels=0.00;FS=10.199;HRun=0;HaplotypeScore=0.9421;InbreedingCoeff=-0.0479;MQ=58.37;MQ0=0;MQRankSum=0.456;QD=10.93;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A271V|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,missense_variant|gCg/gTg|A/V|ENSG00000188976|NOC2L|ENST00000327044|8/19|benign(0.034)|deleterious(0.04)|271/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|6/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889638	.	G	C	14363.41	.	AC=105;AF=0.9211;AN=114;BaseQRankSum=-0.922;DP=427;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3035;InbreedingCoeff=0.0466;MQ=57.19;MQ0=0;MQRankSum=0.153;QD=34.12;ReadPosRankSum=1.663;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|5),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|5/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	889713	.	C	A	5043.64	.	AC=90;AF=0.918;AN=98;BaseQRankSum=-0.018;DP=155;Dels=0.00;FS=4.406;HRun=0;HaplotypeScore=0.0300;InbreedingCoeff=0.0572;MQ=56.80;MQ0=0;MQRankSum=1.329;QD=33.40;ReadPosRankSum=0.873;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|5),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|5/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891021	.	G	A	7780.97	.	AC=101;AF=0.9182;AN=110;BaseQRankSum=0.260;DP=242;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1735;InbreedingCoeff=-0.0202;MQ=58.75;MQ0=0;MQRankSum=-0.704;QD=33.11;ReadPosRankSum=0.580;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|6),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|4),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891059	.	C	T	8049.27	.	AC=70;AF=0.5932;AN=118;BaseQRankSum=0.106;DP=392;Dels=0.00;FS=5.538;HRun=2;HaplotypeScore=0.1844;InbreedingCoeff=0.1314;MQ=58.93;MQ0=0;MQRankSum=-2.097;QD=26.74;ReadPosRankSum=0.989;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|6),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|4),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891401	.	G	A	2441.56	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.910;DP=6853;DS;Dels=0.00;FS=20.474;HRun=4;HaplotypeScore=2.8477;InbreedingCoeff=-0.0084;MQ=58.69;MQ0=0;MQRankSum=2.695;QD=14.45;ReadPosRankSum=2.367;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|5),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|5),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|3),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891620	.	C	A	630.55	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.211;DP=3333;Dels=0.00;FS=17.146;HRun=0;HaplotypeScore=2.5646;InbreedingCoeff=-0.0084;MQ=59.15;MQ0=0;MQRankSum=0.979;QD=8.19;ReadPosRankSum=2.951;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891898	.	T	C	58.0	.	AC=2;AF=0.026;AN=78;BaseQRankSum=-1.208;DP=130;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0256;InbreedingCoeff=-0.1375;MQ=58.94;MQ0=0;MQRankSum=0.462;QD=4.46;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	891945	.	A	G	1861.84	.	AC=44;AF=0.550;AN=80;BaseQRankSum=-1.331;DP=117;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1025;InbreedingCoeff=0.1989;MQ=59.45;MQ0=0;MQRankSum=-0.841;QD=24.82;ReadPosRankSum=0.357;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892095	.	C	T	592.96	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.068;DP=1006;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5011;InbreedingCoeff=-0.0379;MQ=59.11;MQ0=0;MQRankSum=0.441;QD=14.82;ReadPosRankSum=1.641;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892141	.	C	T	66.06	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.417;DP=1605;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9164;InbreedingCoeff=-0.0175;MQ=59.28;MQ0=0;MQRankSum=0.188;QD=3.15;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892237	.	C	A	5045.9	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=2.206;DP=4638;DS;Dels=0.00;FS=16.397;HRun=0;HaplotypeScore=2.4024;InbreedingCoeff=-0.0170;MQ=59.24;MQ0=0;MQRankSum=2.024;QD=16.22;ReadPosRankSum=-3.730;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892460	.	G	C	4504.79	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=2.877;DP=3730;Dels=0.00;FS=1.037;HRun=0;HaplotypeScore=2.4668;InbreedingCoeff=-0.0435;MQ=59.20;MQ0=0;MQRankSum=1.411;QD=15.17;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892470	.	C	T	571.4	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.526;DP=3581;Dels=0.00;FS=5.690;HRun=0;HaplotypeScore=4.5258;InbreedingCoeff=-0.0084;MQ=59.15;MQ0=0;MQRankSum=0.418;QD=11.90;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892471	.	G	A	2720.48	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-7.069;DP=3602;Dels=0.00;FS=2.243;HRun=0;HaplotypeScore=2.7847;InbreedingCoeff=0.4828;MQ=59.14;MQ0=0;MQRankSum=-0.017;QD=13.95;ReadPosRankSum=-0.355;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892724	.	C	T	85.66	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.766;DP=1274;Dels=0.00;FS=3.424;HRun=1;HaplotypeScore=0.8538;InbreedingCoeff=-0.0064;MQ=58.33;MQ0=0;MQRankSum=0.065;QD=14.28;ReadPosRankSum=-0.872;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	892745	.	G	A	33455.23	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=-1.159;DP=989;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3493;InbreedingCoeff=-0.0478;MQ=58.30;MQ0=0;MQRankSum=0.300;QD=33.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	893719	.	G	A	126.7	.	AC=10;AF=0.833;AN=12;BaseQRankSum=-0.198;DP=10;Dels=0.00;FS=3.680;HRun=0;HaplotypeScore=0.1223;MQ=57.66;MQ0=0;MQRankSum=-1.495;QD=21.12;ReadPosRankSum=0.198;EFF=EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	894027	.	G	A	256.69	.	AC=1;AF=0.012;AN=82;BaseQRankSum=-0.446;DP=427;Dels=0.00;FS=4.334;HRun=2;HaplotypeScore=0.2194;InbreedingCoeff=-0.0706;MQ=57.55;MQ0=0;MQRankSum=0.775;QD=18.34;ReadPosRankSum=-0.924;EFF=EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	894330	.	G	A	79.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.248;DP=1450;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7814;InbreedingCoeff=-0.0087;MQ=58.82;MQ0=0;MQRankSum=0.499;QD=7.23;ReadPosRankSum=0.368;EFF=EXON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P53L|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,missense_variant|cCg/cTg|P/L|ENSG00000188976|NOC2L|ENST00000327044|2/19|benign(0.001)|tolerated(0.41)|53/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|2/7||||processed_transcript|1
chr1	894519	.	G	A	127.69	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.782;DP=1334;Dels=0.00;FS=1.737;HRun=1;HaplotypeScore=0.3864;InbreedingCoeff=-0.0205;MQ=58.98;MQ0=0;MQRankSum=0.710;QD=6.72;ReadPosRankSum=0.813;EFF=INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|1),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|1),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	894573	.	G	A	31559.56	.	AC=101;AF=0.8417;AN=120;BaseQRankSum=-0.317;DP=1219;Dels=0.00;FS=2.978;HRun=0;HaplotypeScore=0.8111;InbreedingCoeff=0.1756;MQ=58.45;MQ0=0;MQRankSum=-0.591;QD=27.47;ReadPosRankSum=-0.806;EFF=INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|1),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|1),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	894719	.	C	T	134.46	.	AC=5;AF=0.0463;AN=108;BaseQRankSum=-1.930;DP=230;Dels=0.00;FS=6.502;HRun=0;HaplotypeScore=0.2397;InbreedingCoeff=0.1830;MQ=54.07;MQ0=0;MQRankSum=-0.173;QD=8.40;ReadPosRankSum=1.316;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	894890	.	A	AAGAC	433.26	.	AC=10;AF=1.00;AN=10;DP=6;FS=0.000;HRun=0;HaplotypeScore=9.9355;MQ=29.00;MQ0=0;QD=72.21;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	895706	.	G	A	654.83	.	AC=24;AF=0.857;AN=28;BaseQRankSum=-0.382;DP=28;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1332;InbreedingCoeff=0.2034;MQ=55.74;MQ0=0;MQRankSum=1.582;QD=26.19;ReadPosRankSum=1.255;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	895755	.	A	AG	836.52	.	AC=32;AF=0.941;AN=34;BaseQRankSum=-1.595;DP=39;FS=0.000;HRun=6;HaplotypeScore=8.1200;InbreedingCoeff=0.0511;MQ=54.87;MQ0=0;MQRankSum=1.595;QD=24.60;ReadPosRankSum=-1.456;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	896476	.	A	G	230.97	.	AC=14;AF=1.000;AN=14;DP=11;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=57.87;MQ0=0;QD=21.00;EFF=INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|1),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	896950	.	C	A	1565.88	.	AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.726;DP=1397;Dels=0.00;FS=5.899;HRun=0;HaplotypeScore=0.8800;InbreedingCoeff=-0.0557;MQ=59.13;MQ0=0;MQRankSum=0.483;QD=13.27;ReadPosRankSum=2.665;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|2),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	896977	.	G	C	992.92	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=3.226;DP=1654;Dels=0.00;FS=64.681;HRun=1;HaplotypeScore=1.1124;InbreedingCoeff=-0.0302;MQ=59.13;MQ0=0;MQRankSum=0.693;QD=19.09;ReadPosRankSum=-3.945;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|2),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897325	.	G	C	125121.37	.	AC=109;AF=0.9083;AN=120;BaseQRankSum=2.562;DP=4268;Dels=0.00;FS=6.072;HRun=1;HaplotypeScore=2.5759;InbreedingCoeff=0.0992;MQ=58.65;MQ0=0;MQRankSum=-0.923;QD=29.72;ReadPosRankSum=-2.769;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A203|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),UTR_5_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|gcG/gcC|A|ENSG00000187961|KLHL17|ENST00000338591|4/12|||203/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897337	.	C	T	1277.99	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.453;DP=4287;Dels=0.00;FS=8.422;HRun=0;HaplotypeScore=2.3521;InbreedingCoeff=-0.0084;MQ=58.59;MQ0=0;MQRankSum=0.646;QD=14.36;ReadPosRankSum=0.556;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),START_GAINED(LOW||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S207|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|agC/agT|S|ENSG00000187961|KLHL17|ENST00000338591|4/12|||207/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897460	.	A	C	4476.36	.	AC=24;AF=0.2069;AN=116;BaseQRankSum=-6.649;DP=4306;DS;Dels=0.00;FS=1182.881;HRun=6;HaplotypeScore=18.5719;InbreedingCoeff=-0.2955;MQ=53.12;MQ0=0;MQRankSum=-6.585;QD=1.27;ReadPosRankSum=-5.387;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897465	.	A	C	207.3	.	AC=8;AF=0.0678;AN=118;BaseQRankSum=-6.006;DP=4323;DS;Dels=0.00;FS=207.986;HRun=4;HaplotypeScore=15.9325;InbreedingCoeff=-0.0865;MQ=53.13;MQ0=0;MQRankSum=-13.595;QD=0.15;ReadPosRankSum=-11.475;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897470	.	A	C	60.04	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-10.911;DP=4336;DS;Dels=0.00;FS=267.922;HRun=4;HaplotypeScore=16.3920;InbreedingCoeff=-0.0465;MQ=53.18;MQ0=0;MQRankSum=-11.192;QD=0.22;ReadPosRankSum=-11.844;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897564	.	T	C	105645.82	.	AC=111;AF=0.9407;AN=118;BaseQRankSum=-0.165;DP=3668;DS;Dels=0.00;FS=4.440;HRun=1;HaplotypeScore=1.8075;InbreedingCoeff=0.1915;MQ=54.46;MQ0=0;MQRankSum=3.570;QD=29.65;ReadPosRankSum=-1.056;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897641	.	C	T	42.61	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.313;DP=2743;DS;Dels=0.00;FS=9.036;HRun=0;HaplotypeScore=1.2616;InbreedingCoeff=-0.0088;MQ=55.91;MQ0=0;MQRankSum=0.432;QD=3.87;ReadPosRankSum=0.049;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897730	.	C	T	1850.25	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.726;DP=3106;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.1479;InbreedingCoeff=-0.0256;MQ=58.41;MQ0=0;MQRankSum=-0.353;QD=12.94;ReadPosRankSum=-0.223;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897738	.	C	T	5799.05	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=1.153;DP=3157;Dels=0.00;FS=6.498;HRun=2;HaplotypeScore=2.6795;InbreedingCoeff=0.1964;MQ=58.52;MQ0=0;MQRankSum=1.044;QD=16.11;ReadPosRankSum=-1.772;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L239|642|KLHL17|protein_coding|CODING|ENST00000338591|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L9|412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|Ctg/Ttg|L|ENSG00000187961|KLHL17|ENST00000338591|5/12|||239/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	897879	.	C	T	1100.72	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.411;DP=1081;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7665;InbreedingCoeff=-0.0357;MQ=58.62;MQ0=0;MQRankSum=0.745;QD=12.80;ReadPosRankSum=2.064;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|4),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|5),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898068	.	G	C	79.28	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.132;DP=1385;Dels=0.00;FS=2.990;HRun=1;HaplotypeScore=0.9318;InbreedingCoeff=0.8872;MQ=57.94;MQ0=0;MQRankSum=0.935;QD=19.82;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|4),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|5),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898323	.	T	C	52014.58	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=-0.884;DP=1603;Dels=0.00;FS=3.229;HRun=1;HaplotypeScore=0.9054;InbreedingCoeff=-0.0448;MQ=58.52;MQ0=0;MQRankSum=-0.998;QD=32.45;ReadPosRankSum=2.785;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|5),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|6),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898467	.	C	T	1510.84	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-0.034;DP=1255;Dels=0.00;FS=4.507;HRun=0;HaplotypeScore=0.8357;InbreedingCoeff=-0.0475;MQ=58.85;MQ0=0;MQRankSum=-1.026;QD=13.49;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|5),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|6),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=synonymous_variant&NMD_transcript_variant|ccC/ccT|P|ENSG00000187961|KLHL17|ENST00000466300|2/6|||83/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898603	.	C	G	116.84	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=-8.523;DP=3456;Dels=0.00;FS=28.932;HRun=2;HaplotypeScore=4.3555;InbreedingCoeff=-0.0746;MQ=57.81;MQ0=0;MQRankSum=-3.388;QD=0.70;ReadPosRankSum=-5.743;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gGg|A156G|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gGg|A386G|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=missense_variant&NMD_transcript_variant|Cgg/Ggg|R/G|ENSG00000187961|KLHL17|ENST00000466300|2/6|unknown(0)|deleterious(0)|129/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,missense_variant|gCg/gGg|A/G|ENSG00000187961|KLHL17|ENST00000338591|7/12|possibly_damaging(0.8)|tolerated(0.13)|386/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898604	.	G	A	684.72	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.572;DP=3527;Dels=0.00;FS=8.272;HRun=0;HaplotypeScore=4.4131;InbreedingCoeff=-0.0111;MQ=57.83;MQ0=0;MQRankSum=0.825;QD=9.92;ReadPosRankSum=-0.003;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A156|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A386|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=missense_variant&NMD_transcript_variant|cGg/cAg|R/Q|ENSG00000187961|KLHL17|ENST00000466300|2/6|unknown(0)|deleterious(0)|129/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|gcG/gcA|A|ENSG00000187961|KLHL17|ENST00000338591|7/12|||386/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898893	.	G	C	345.84	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.109;DP=2327;Dels=0.00;FS=1.347;HRun=0;HaplotypeScore=1.8649;InbreedingCoeff=-0.0084;MQ=58.71;MQ0=0;MQRankSum=0.616;QD=12.81;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	898934	.	G	A	47.08	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.111;DP=1477;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6015;InbreedingCoeff=-0.0091;MQ=58.84;MQ0=0;MQRankSum=0.087;QD=5.89;ReadPosRankSum=-1.045;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899000	.	C	T	654.34	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=-0.932;DP=651;Dels=0.00;FS=1.229;HRun=0;HaplotypeScore=0.5946;InbreedingCoeff=0.3177;MQ=58.35;MQ0=0;MQRankSum=0.454;QD=16.36;ReadPosRankSum=0.885;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899318	.	C	T	428.77	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.231;DP=2100;Dels=0.00;FS=29.933;HRun=0;HaplotypeScore=1.6653;InbreedingCoeff=-0.0087;MQ=58.94;MQ0=0;MQRankSum=-0.016;QD=10.99;ReadPosRankSum=-1.614;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P228|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P458|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|4/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187961|KLHL17|ENST00000338591|9/12|||458/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899374	.	G	A	298.41	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.204;DP=2588;Dels=0.00;FS=1.169;HRun=1;HaplotypeScore=1.4609;InbreedingCoeff=-0.0084;MQ=58.81;MQ0=0;MQRankSum=0.082;QD=10.29;ReadPosRankSum=2.022;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R247Q|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R477Q|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|4/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,missense_variant|cGa/cAa|R/Q|ENSG00000187961|KLHL17|ENST00000338591|9/12|possibly_damaging(0.886)|deleterious(0.03)|477/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899515	.	C	T	554.46	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.826;DP=4376;Dels=0.00;FS=0.766;HRun=0;HaplotypeScore=2.1786;InbreedingCoeff=-0.0084;MQ=58.98;MQ0=0;MQRankSum=-0.199;QD=13.86;ReadPosRankSum=2.919;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|2),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y261|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y491|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|5/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|taC/taT|Y|ENSG00000187961|KLHL17|ENST00000338591|10/12|||491/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899648	.	C	T	506.51	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.603;DP=2206;Dels=0.00;FS=1.040;HRun=0;HaplotypeScore=2.2848;InbreedingCoeff=-0.0084;MQ=57.02;MQ0=0;MQRankSum=0.240;QD=14.90;ReadPosRankSum=1.277;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|9),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|10),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1
chr1	899824	.	C	T	386.57	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=-1.360;DP=1027;Dels=0.00;FS=0.938;HRun=0;HaplotypeScore=0.7940;InbreedingCoeff=-0.0327;MQ=52.55;MQ0=0;MQRankSum=2.078;QD=10.17;ReadPosRankSum=-2.959;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N308|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N538|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|6/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000187961|KLHL17|ENST00000338591|11/12|||538/642|protein_coding|1
chr1	899926	.	GC	G	146.78	.	AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.149;DP=401;FS=8.501;HRun=1;HaplotypeScore=98.5276;InbreedingCoeff=-0.0768;MQ=46.11;MQ0=0;MQRankSum=-4.025;QD=4.32;ReadPosRankSum=-1.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899928	.	G	C	10304.35	.	AC=95;AF=0.8636;AN=110;BaseQRankSum=-2.647;DP=394;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9435;InbreedingCoeff=-0.0052;MQ=45.90;MQ0=0;MQRankSum=-1.207;QD=26.35;ReadPosRankSum=1.974;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899937	.	G	T	7323.3	.	AC=86;AF=0.860;AN=100;BaseQRankSum=-1.886;DP=301;Dels=0.00;FS=4.882;HRun=0;HaplotypeScore=1.0717;InbreedingCoeff=0.2201;MQ=45.04;MQ0=0;MQRankSum=-1.460;QD=25.61;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899938	.	G	C	7723.52	.	AC=86;AF=0.860;AN=100;BaseQRankSum=-1.269;DP=292;Dels=0.00;FS=6.709;HRun=1;HaplotypeScore=0.9273;InbreedingCoeff=0.2346;MQ=45.14;MQ0=0;MQRankSum=-2.046;QD=27.78;ReadPosRankSum=2.689;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899942	.	G	A	9223.42	.	AC=87;AF=0.8529;AN=102;BaseQRankSum=-0.795;DP=333;Dels=0.00;FS=4.035;HRun=0;HaplotypeScore=0.7409;InbreedingCoeff=0.1074;MQ=43.28;MQ0=0;MQRankSum=-1.361;QD=28.38;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899943	.	G	C	99.41	.	AC=3;AF=0.0294;AN=102;BaseQRankSum=-1.668;DP=334;Dels=0.00;FS=4.946;HRun=0;HaplotypeScore=0.6513;InbreedingCoeff=-0.0759;MQ=42.96;MQ0=0;MQRankSum=-3.741;QD=2.76;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899959	.	G	GC	686.45	.	AC=19;AF=0.190;AN=100;BaseQRankSum=-3.215;DP=298;FS=12.605;HRun=0;HaplotypeScore=100.2656;InbreedingCoeff=-0.1846;MQ=45.28;MQ0=0;MQRankSum=-5.322;QD=4.40;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899960	.	T	C	416.06	.	AC=19;AF=0.190;AN=100;BaseQRankSum=3.474;DP=298;Dels=0.00;FS=12.762;HRun=0;HaplotypeScore=0.3615;InbreedingCoeff=-0.1710;MQ=45.28;MQ0=0;MQRankSum=-6.659;QD=2.87;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899974	.	G	A	175.25	.	AC=17;AF=0.170;AN=100;BaseQRankSum=1.366;DP=246;Dels=0.00;FS=8.615;HRun=0;HaplotypeScore=0.2560;InbreedingCoeff=-0.1500;MQ=45.05;MQ0=0;MQRankSum=-5.035;QD=1.79;ReadPosRankSum=-2.296;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899975	.	C	G	161.84	.	AC=18;AF=0.180;AN=100;BaseQRankSum=1.074;DP=239;Dels=0.00;FS=8.632;HRun=1;HaplotypeScore=0.2414;InbreedingCoeff=-0.1746;MQ=44.67;MQ0=0;MQRankSum=-6.140;QD=1.54;ReadPosRankSum=-2.132;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899987	.	GGATGT	G	805.24	.	AC=10;AF=0.102;AN=98;BaseQRankSum=-2.007;DP=183;FS=4.301;HRun=0;HaplotypeScore=71.0169;InbreedingCoeff=0.1259;MQ=41.55;MQ0=0;MQRankSum=-2.599;QD=19.64;ReadPosRankSum=-2.063;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	899998	.	G	C	172.67	.	AC=3;AF=0.0288;AN=104;BaseQRankSum=-3.045;DP=165;Dels=0.01;FS=6.898;HRun=1;HaplotypeScore=3.2446;InbreedingCoeff=-0.1274;MQ=38.58;MQ0=0;MQRankSum=-2.770;QD=7.85;ReadPosRankSum=2.697;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900000	.	G	GAA	4516.13	.	AC=82;AF=0.8039;AN=102;BaseQRankSum=-0.011;DP=158;FS=8.933;HRun=0;HaplotypeScore=53.7512;InbreedingCoeff=0.0958;MQ=37.58;MQ0=0;MQRankSum=-2.778;QD=29.91;ReadPosRankSum=0.180;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900001	.	G	A	1769.07	.	AC=55;AF=0.561;AN=98;BaseQRankSum=-1.838;DP=158;Dels=0.00;FS=12.659;HRun=1;HaplotypeScore=4.3165;InbreedingCoeff=0.0703;MQ=37.58;MQ0=0;MQRankSum=-1.578;QD=15.38;ReadPosRankSum=-0.873;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900009	.	C	G	1460.59	.	AC=51;AF=0.510;AN=100;BaseQRankSum=1.557;DP=154;Dels=0.00;FS=5.254;HRun=6;HaplotypeScore=3.7869;InbreedingCoeff=0.1584;MQ=37.06;MQ0=0;MQRankSum=-2.397;QD=14.75;ReadPosRankSum=1.027;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900009	.	CG	C	3423.69	.	AC=75;AF=0.765;AN=98;BaseQRankSum=-1.591;DP=149;FS=3.362;HRun=6;HaplotypeScore=53.0225;InbreedingCoeff=-0.0140;MQ=37.05;MQ0=0;MQRankSum=0.377;QD=24.45;ReadPosRankSum=3.509;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900010	.	G	GC	2274.92	.	AC=67;AF=0.684;AN=98;BaseQRankSum=-2.660;DP=149;FS=0.000;HRun=1;HaplotypeScore=58.6576;InbreedingCoeff=0.1712;MQ=37.05;MQ0=0;MQRankSum=0.765;QD=18.35;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900012	.	G	A	52.89	.	AC=9;AF=0.092;AN=98;BaseQRankSum=-1.584;DP=144;Dels=0.00;FS=9.518;HRun=0;HaplotypeScore=1.9499;InbreedingCoeff=-0.1191;MQ=37.30;MQ0=0;MQRankSum=-1.274;QD=1.56;ReadPosRankSum=-3.899;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900018	.	G	A	202.57	.	AC=3;AF=0.033;AN=90;BaseQRankSum=-0.005;DP=138;Dels=0.00;FS=14.921;HRun=0;HaplotypeScore=2.7642;InbreedingCoeff=-0.1390;MQ=37.35;MQ0=0;MQRankSum=-2.631;QD=11.25;ReadPosRankSum=-0.202;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900025	.	GGATGT	G	524.76	.	AC=16;AF=0.174;AN=92;BaseQRankSum=3.838;DP=133;FS=8.461;HRun=0;HaplotypeScore=57.1337;InbreedingCoeff=-0.0789;MQ=37.07;MQ0=0;MQRankSum=-2.025;QD=12.49;ReadPosRankSum=0.267;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900036	.	C	G	56.0	.	AC=8;AF=0.095;AN=84;BaseQRankSum=-0.360;DP=115;Dels=0.02;FS=4.181;HRun=3;HaplotypeScore=2.4570;InbreedingCoeff=0.0759;MQ=37.96;MQ0=0;MQRankSum=-2.183;QD=3.73;ReadPosRankSum=1.383;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900045	.	G	T	197.92	.	AC=12;AF=0.158;AN=76;BaseQRankSum=-0.033;DP=97;Dels=0.00;FS=9.602;HRun=0;HaplotypeScore=0.8494;InbreedingCoeff=-0.1283;MQ=36.39;MQ0=0;MQRankSum=-3.050;QD=6.60;ReadPosRankSum=0.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900046	.	G	C	221.18	.	AC=14;AF=0.194;AN=72;BaseQRankSum=0.606;DP=95;Dels=0.00;FS=15.119;HRun=1;HaplotypeScore=0.8152;InbreedingCoeff=-0.0844;MQ=36.53;MQ0=0;MQRankSum=-3.254;QD=6.91;ReadPosRankSum=0.931;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900047	.	CG	C	209.92	.	AC=15;AF=0.208;AN=72;BaseQRankSum=1.707;DP=88;FS=0.000;HRun=6;HaplotypeScore=49.2935;InbreedingCoeff=-0.1925;MQ=36.21;MQ0=0;MQRankSum=-2.511;QD=4.47;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900050	.	G	A	240.82	.	AC=14;AF=0.226;AN=62;BaseQRankSum=1.097;DP=84;Dels=0.00;FS=15.435;HRun=0;HaplotypeScore=0.6581;InbreedingCoeff=-0.0898;MQ=34.67;MQ0=0;MQRankSum=-1.036;QD=8.03;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900065	.	A	C	247.12	.	AC=17;AF=0.304;AN=56;BaseQRankSum=1.516;DP=63;Dels=0.00;FS=9.830;HRun=0;HaplotypeScore=2.1490;InbreedingCoeff=-0.0549;MQ=32.56;MQ0=0;MQRankSum=-0.918;QD=7.06;ReadPosRankSum=2.224;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900068	.	TGCTGCC	T	518.39	.	AC=13;AF=0.217;AN=60;BaseQRankSum=4.713;DP=59;FS=14.526;HRun=0;HaplotypeScore=44.2811;InbreedingCoeff=0.0509;MQ=31.33;MQ0=0;MQRankSum=-0.386;QD=28.80;ReadPosRankSum=4.120;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900083	.	G	T	196.8	.	AC=12;AF=0.286;AN=42;BaseQRankSum=-2.303;DP=46;Dels=0.00;FS=9.918;HRun=0;HaplotypeScore=1.2000;InbreedingCoeff=0.0257;MQ=29.00;MQ0=0;MQRankSum=0.317;QD=10.36;ReadPosRankSum=1.627;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900084	.	G	C	236.51	.	AC=14;AF=0.350;AN=40;BaseQRankSum=-0.904;DP=46;Dels=0.00;FS=12.035;HRun=1;HaplotypeScore=1.2233;InbreedingCoeff=0.0591;MQ=29.00;MQ0=0;MQRankSum=-0.215;QD=11.83;ReadPosRankSum=1.420;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900085	.	C	G	54.45	.	AC=7;AF=0.175;AN=40;BaseQRankSum=1.312;DP=45;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.9242;InbreedingCoeff=0.1696;MQ=29.00;MQ0=0;MQRankSum=0.641;QD=7.78;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900086	.	G	GC	66.18	.	AC=9;AF=0.265;AN=34;BaseQRankSum=-0.405;DP=42;FS=3.909;HRun=1;HaplotypeScore=46.6346;InbreedingCoeff=0.0729;MQ=29.00;MQ0=0;MQRankSum=0.231;QD=4.41;ReadPosRankSum=-0.925;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900089	.	G	C	230.72	.	AC=14;AF=0.500;AN=28;BaseQRankSum=0.692;DP=39;Dels=0.00;FS=10.780;HRun=0;HaplotypeScore=0.8484;InbreedingCoeff=0.2201;MQ=29.00;MQ0=0;MQRankSum=0.165;QD=14.42;ReadPosRankSum=0.495;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900103	.	A	C	245.84	.	AC=13;AF=0.650;AN=20;BaseQRankSum=2.098;DP=29;Dels=0.00;FS=4.393;HRun=0;HaplotypeScore=1.1682;InbreedingCoeff=-0.0533;MQ=29.00;MQ0=0;MQRankSum=2.098;QD=15.37;ReadPosRankSum=0.146;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900112	.	C	G	149.58	.	AC=10;AF=0.556;AN=18;BaseQRankSum=1.027;DP=24;Dels=0.04;FS=2.276;HRun=3;HaplotypeScore=0.9865;MQ=29.00;MQ0=0;MQRankSum=1.027;QD=12.47;ReadPosRankSum=0.201;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900115	.	G	A	35.09	.	AC=5;AF=0.227;AN=22;BaseQRankSum=2.382;DP=23;Dels=0.00;FS=13.570;HRun=1;HaplotypeScore=1.7631;InbreedingCoeff=0.1307;MQ=29.00;MQ0=0;MQRankSum=-0.361;QD=7.02;ReadPosRankSum=-1.083;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900123	.	C	G	41.39	.	AC=5;AF=0.357;AN=14;BaseQRankSum=1.931;DP=20;Dels=0.00;FS=14.771;HRun=6;HaplotypeScore=1.5461;MQ=29.00;MQ0=0;MQRankSum=0.000;QD=5.17;ReadPosRankSum=-0.382;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900123	.	CG	C	239.86	.	AC=12;AF=0.600;AN=20;BaseQRankSum=0.715;DP=20;FS=2.363;HRun=6;HaplotypeScore=37.1615;InbreedingCoeff=0.0592;MQ=29.00;MQ0=0;MQRankSum=-0.965;QD=17.13;ReadPosRankSum=0.627;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900161	.	C	G	95.96	.	AC=3;AF=0.041;AN=74;BaseQRankSum=-0.808;DP=152;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.5011;InbreedingCoeff=-0.1315;MQ=55.56;MQ0=0;MQRankSum=1.024;QD=4.17;ReadPosRankSum=-2.738;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900188	.	C	G	109.47	.	AC=2;AF=0.021;AN=96;BaseQRankSum=0.425;DP=319;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.5571;InbreedingCoeff=-0.0765;MQ=55.58;MQ0=0;MQRankSum=-4.308;QD=9.95;ReadPosRankSum=-1.562;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900191	.	G	A	78.75	.	AC=2;AF=0.020;AN=98;BaseQRankSum=0.169;DP=359;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6619;InbreedingCoeff=-0.0713;MQ=55.88;MQ0=0;MQRankSum=-3.973;QD=7.16;ReadPosRankSum=-0.841;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900199	.	C	G	122.69	.	AC=2;AF=0.0196;AN=102;BaseQRankSum=-0.625;DP=419;Dels=0.00;FS=5.991;HRun=6;HaplotypeScore=0.9712;InbreedingCoeff=-0.0705;MQ=55.82;MQ0=0;MQRankSum=-4.226;QD=11.15;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900200	.	G	GC	138.36	.	AC=2;AF=0.0192;AN=104;BaseQRankSum=4.004;DP=447;FS=5.745;HRun=1;HaplotypeScore=63.8129;InbreedingCoeff=-0.0683;MQ=55.87;MQ0=0;MQRankSum=-4.054;QD=10.64;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900205	.	T	C	3848.55	.	AC=28;AF=0.2642;AN=106;BaseQRankSum=3.976;DP=500;Dels=0.00;FS=4.311;HRun=2;HaplotypeScore=0.8450;InbreedingCoeff=-0.0127;MQ=56.04;MQ0=0;MQRankSum=2.371;QD=15.21;ReadPosRankSum=0.624;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900208	.	G	A	196.8	.	AC=3;AF=0.0278;AN=108;BaseQRankSum=-1.850;DP=545;Dels=0.00;FS=3.034;HRun=0;HaplotypeScore=0.9217;InbreedingCoeff=-0.0711;MQ=55.89;MQ0=0;MQRankSum=-1.612;QD=8.56;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900252	.	G	A	2492.99	.	AC=7;AF=0.0593;AN=118;BaseQRankSum=0.859;DP=1112;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6311;InbreedingCoeff=-0.0857;MQ=55.70;MQ0=0;MQRankSum=2.953;QD=13.33;ReadPosRankSum=-0.555;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900285	.	C	T	49972.75	.	AC=105;AF=0.9052;AN=116;BaseQRankSum=-3.461;DP=1713;Dels=0.00;FS=2.048;HRun=0;HaplotypeScore=2.6694;InbreedingCoeff=0.0387;MQ=55.27;MQ0=0;MQRankSum=-1.138;QD=29.80;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900286	.	A	G	53795.91	.	AC=111;AF=0.9569;AN=116;BaseQRankSum=-1.271;DP=1744;Dels=0.00;FS=6.893;HRun=1;HaplotypeScore=2.7132;InbreedingCoeff=-0.0679;MQ=55.34;MQ0=0;MQRankSum=0.681;QD=30.85;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900298	.	C	G	1312.84	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.430;DP=2069;Dels=0.00;FS=2.014;HRun=1;HaplotypeScore=1.8253;InbreedingCoeff=0.1410;MQ=55.23;MQ0=0;MQRankSum=1.938;QD=10.67;ReadPosRankSum=-0.720;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900319	.	G	A	830.69	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=0.864;DP=2658;Dels=0.00;FS=5.182;HRun=0;HaplotypeScore=1.8883;InbreedingCoeff=-0.0417;MQ=56.04;MQ0=0;MQRankSum=2.734;QD=10.93;ReadPosRankSum=1.705;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	900397	.	C	T	2009.84	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.145;DP=5436;DS;Dels=0.00;FS=0.454;HRun=0;HaplotypeScore=4.5718;InbreedingCoeff=-0.0195;MQ=57.26;MQ0=0;MQRankSum=1.619;QD=12.72;ReadPosRankSum=-0.157;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N355|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N585|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000187961|KLHL17|ENST00000338591|12/12|||585/642|protein_coding|1
chr1	900505	.	G	C	36708.31	.	AC=34;AF=0.2881;AN=118;BaseQRankSum=3.779;DP=6012;DS;Dels=0.00;FS=16.118;HRun=1;HaplotypeScore=4.6415;InbreedingCoeff=-0.1592;MQ=56.94;MQ0=0;MQRankSum=2.324;QD=13.04;ReadPosRankSum=-1.518;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V391|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V621|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|gtG/gtC|V|ENSG00000187961|KLHL17|ENST00000338591|12/12|||621/642|protein_coding|1
chr1	900560	.	A	C	336.55	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=-16.919;DP=3961;DS;Dels=0.00;FS=94.082;HRun=2;HaplotypeScore=2.4690;InbreedingCoeff=-0.1027;MQ=56.02;MQ0=0;MQRankSum=-0.133;QD=2.37;ReadPosRankSum=-4.673;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T410P|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T640P|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187961|KLHL17|ENST00000338591|12/12|unknown(0)|deleterious(0.02)|640/642|protein_coding|1
chr1	900717	.	CTTAT	C	9074.2	.	AC=69;AF=0.6053;AN=114;BaseQRankSum=10.277;DP=412;FS=7.468;HRun=0;HaplotypeScore=48.3915;InbreedingCoeff=0.0298;MQ=48.25;MQ0=0;MQRankSum=-9.614;QD=26.85;ReadPosRankSum=3.811;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	900723	.	T	G	285.98	.	AC=14;AF=0.1228;AN=114;BaseQRankSum=-3.773;DP=321;Dels=0.00;FS=2.147;HRun=0;HaplotypeScore=11.3195;InbreedingCoeff=-0.1788;MQ=46.06;MQ0=0;MQRankSum=4.705;QD=2.95;ReadPosRankSum=-6.059;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	900730	.	G	A	7842.1	.	AC=100;AF=0.8621;AN=116;BaseQRankSum=-0.675;DP=275;Dels=0.00;FS=1.534;HRun=0;HaplotypeScore=5.4770;InbreedingCoeff=0.2758;MQ=43.76;MQ0=0;MQRankSum=-4.770;QD=29.93;ReadPosRankSum=-1.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	900972	.	T	G	837.46	.	AC=38;AF=0.950;AN=40;BaseQRankSum=1.091;DP=28;Dels=0.00;FS=5.863;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=-0.0011;MQ=56.62;MQ0=0;MQRankSum=1.091;QD=32.21;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	901023	.	T	C	668.0	.	AC=30;AF=0.882;AN=34;BaseQRankSum=0.039;DP=25;Dels=0.00;FS=13.318;HRun=0;HaplotypeScore=0.1562;InbreedingCoeff=-0.0502;MQ=59.07;MQ0=0;MQRankSum=-1.123;QD=29.04;ReadPosRankSum=-2.053;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	901046	.	ACC	A	367.24	.	AC=14;AF=0.368;AN=38;BaseQRankSum=3.349;DP=34;FS=3.319;HRun=4;HaplotypeScore=8.5629;InbreedingCoeff=0.2418;MQ=57.94;MQ0=0;MQRankSum=-0.562;QD=26.23;ReadPosRankSum=0.832;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1
chr1	901460	.	C	T	32.18	.	AC=2;AF=0.045;AN=44;BaseQRankSum=0.046;DP=29;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0879;InbreedingCoeff=-0.0076;MQ=59.20;MQ0=0;MQRankSum=0.231;QD=16.09;ReadPosRankSum=-1.435;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	901559	.	G	A	1182.94	.	AC=46;AF=0.920;AN=50;BaseQRankSum=0.433;DP=38;Dels=0.00;FS=2.501;HRun=0;HaplotypeScore=0.1286;InbreedingCoeff=-0.0789;MQ=56.89;MQ0=0;MQRankSum=-0.974;QD=31.97;ReadPosRankSum=-0.704;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	901607	.	C	G	1775.67	.	AC=57;AF=0.983;AN=58;BaseQRankSum=-0.817;DP=56;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.0000;InbreedingCoeff=-0.1683;MQ=56.62;MQ0=0;MQRankSum=-0.443;QD=32.28;ReadPosRankSum=-0.303;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	901652	.	A	G	2979.53	.	AC=72;AF=1.000;AN=72;DP=87;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0518;InbreedingCoeff=-0.1163;MQ=57.30;MQ0=0;QD=34.65;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	901806	.	G	C	1993.1	.	AC=13;AF=0.1204;AN=108;BaseQRankSum=0.578;DP=624;Dels=0.00;FS=2.492;HRun=3;HaplotypeScore=0.2501;InbreedingCoeff=0.2481;MQ=58.77;MQ0=0;MQRankSum=1.452;QD=19.16;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	901919	.	A	C	43.36	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-7.616;DP=1450;Dels=0.00;FS=55.854;HRun=1;HaplotypeScore=0.9087;InbreedingCoeff=-0.0627;MQ=58.76;MQ0=0;MQRankSum=-1.305;QD=0.46;ReadPosRankSum=-4.128;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379409|1/15|possibly_damaging(0.471)|deleterious(0.01)|3/663|protein_coding|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379407|1/15|benign(0.331)|deleterious(0.01)|3/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379410|1/16|benign(0.444)|deleterious(0.01)|3/611|protein_coding|1
chr1	902043	.	G	A	169.05	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.369;DP=777;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0432;InbreedingCoeff=-0.0431;MQ=58.28;MQ0=0;MQRankSum=0.826;QD=5.45;ReadPosRankSum=-0.446;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|1),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|1),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|1),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	902069	.	T	C	177.69	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.199;DP=717;Dels=0.00;FS=3.490;HRun=4;HaplotypeScore=0.5354;InbreedingCoeff=-0.0340;MQ=58.23;MQ0=0;MQRankSum=0.502;QD=7.11;ReadPosRankSum=0.208;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|1),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|1),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|1),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	902108	.	C	T	116.44	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.766;DP=558;Dels=0.00;FS=3.848;HRun=0;HaplotypeScore=0.5318;InbreedingCoeff=-0.0325;MQ=58.52;MQ0=0;MQRankSum=-0.417;QD=8.96;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379409|2/15|||36/663|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379407|2/15|||36/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379410|2/16|||36/611|protein_coding|1
chr1	902128	.	C	T	375.73	.	AC=3;AF=0.0254;AN=118;BaseQRankSum=-0.165;DP=545;Dels=0.00;FS=0.993;HRun=1;HaplotypeScore=0.3151;InbreedingCoeff=-0.0508;MQ=58.23;MQ0=0;MQRankSum=0.962;QD=11.39;ReadPosRankSum=-1.116;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379409|2/15|possibly_damaging(0.586)|deleterious(0.01)|43/663|protein_coding|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379407|2/15|benign(0.209)|deleterious(0.01)|43/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379410|2/16|benign(0.209)|deleterious(0.01)|43/611|protein_coding|1
chr1	902288	.	G	A	297.6	.	AC=8;AF=0.083;AN=96;BaseQRankSum=-1.235;DP=169;Dels=0.00;FS=6.677;HRun=0;HaplotypeScore=0.1735;InbreedingCoeff=0.2484;MQ=58.34;MQ0=0;MQRankSum=1.682;QD=12.94;ReadPosRankSum=-1.820;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	905130	.	ATG	A	1155.32	.	AC=23;AF=0.442;AN=52;BaseQRankSum=1.417;DP=60;FS=3.885;HRun=0;HaplotypeScore=17.3266;InbreedingCoeff=0.3250;MQ=54.35;MQ0=0;MQRankSum=-1.757;QD=30.40;ReadPosRankSum=1.061;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	905158	.	TGC	T	181.75	.	AC=10;AF=0.200;AN=50;BaseQRankSum=-3.797;DP=55;FS=1.587;HRun=0;HaplotypeScore=23.4217;InbreedingCoeff=0.1863;MQ=54.38;MQ0=0;MQRankSum=0.194;QD=12.98;ReadPosRankSum=-2.056;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	905165	.	A	G	1906.87	.	AC=48;AF=0.960;AN=50;BaseQRankSum=0.088;DP=59;Dels=0.00;FS=5.156;HRun=0;HaplotypeScore=0.3866;InbreedingCoeff=0.0421;MQ=56.05;MQ0=0;MQRankSum=1.086;QD=32.88;ReadPosRankSum=-1.380;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	905894	.	C	T	1520.95	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.494;DP=3276;Dels=0.00;FS=2.372;HRun=0;HaplotypeScore=1.4299;InbreedingCoeff=-0.0172;MQ=58.58;MQ0=0;MQRankSum=0.861;QD=13.46;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|3),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|3),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|3),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1
chr1	906272	.	A	C	2509.21	.	AC=19;AF=0.1583;AN=120;BaseQRankSum=3.923;DP=937;Dels=0.00;FS=33.565;HRun=4;HaplotypeScore=0.7062;InbreedingCoeff=0.0234;MQ=58.16;MQ0=0;MQRankSum=0.166;QD=10.72;ReadPosRankSum=0.823;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|1),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A166|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A166|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A206|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379409|5/15|||206/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|1/3||||retained_intron|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379407|6/15|||166/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379410|6/16|||166/611|protein_coding|1
chr1	906302	.	C	T	240.96	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.006;DP=838;Dels=0.00;FS=7.521;HRun=0;HaplotypeScore=0.4687;InbreedingCoeff=-0.0191;MQ=58.08;MQ0=0;MQRankSum=-0.315;QD=8.03;ReadPosRankSum=-2.447;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A176|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A176|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A216|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379409|5/15|||216/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|1/3||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379407|6/15|||176/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379410|6/16|||176/611|protein_coding|1
chr1	906850	.	C	T	840.9	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.291;DP=1812;Dels=0.00;FS=2.912;HRun=0;HaplotypeScore=1.3291;InbreedingCoeff=-0.0167;MQ=58.39;MQ0=0;MQRankSum=0.375;QD=15.02;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|3/3||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	906872	.	C	T	490.99	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.837;DP=1326;Dels=0.00;FS=11.727;HRun=3;HaplotypeScore=0.8532;InbreedingCoeff=-0.0185;MQ=58.72;MQ0=0;MQRankSum=0.435;QD=14.88;ReadPosRankSum=0.427;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|3/3||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	906974	.	G	A	150.57	.	AC=2;AF=0.0185;AN=108;BaseQRankSum=0.388;DP=247;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1707;InbreedingCoeff=-0.0985;MQ=58.20;MQ0=0;MQRankSum=0.405;QD=12.55;ReadPosRankSum=0.062;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907023	.	G	A	49.9	.	AC=4;AF=0.048;AN=84;BaseQRankSum=0.466;DP=145;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1426;InbreedingCoeff=0.2013;MQ=59.04;MQ0=0;MQRankSum=0.872;QD=16.63;ReadPosRankSum=-0.015;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907170	.	AG	A	1280.62	.	AC=36;AF=0.3462;AN=104;BaseQRankSum=3.258;DP=132;FS=0.000;HRun=3;HaplotypeScore=8.3225;InbreedingCoeff=0.2957;MQ=57.69;MQ0=0;MQRankSum=0.182;QD=20.99;ReadPosRankSum=0.423;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907609	.	T	C	2023.79	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-2.518;DP=2587;Dels=0.00;FS=0.956;HRun=0;HaplotypeScore=2.5448;InbreedingCoeff=-0.0366;MQ=48.44;MQ0=0;MQRankSum=4.469;QD=10.76;ReadPosRankSum=2.738;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907622	.	G	C	3088.17	.	AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.813;DP=2382;Dels=0.00;FS=1.696;HRun=0;HaplotypeScore=13.8552;InbreedingCoeff=0.2112;MQ=46.67;MQ0=0;MQRankSum=5.413;QD=12.21;ReadPosRankSum=2.166;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907631	.	A	C	2295.85	.	AC=35;AF=0.2917;AN=120;BaseQRankSum=-20.997;DP=2266;Dels=0.00;FS=665.053;HRun=7;HaplotypeScore=7.6604;InbreedingCoeff=-0.4342;MQ=46.08;MQ0=0;MQRankSum=-14.611;QD=1.46;ReadPosRankSum=13.032;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907758	.	A	G	191.93	.	AC=13;AF=0.1140;AN=114;BaseQRankSum=-12.237;DP=1481;Dels=0.01;FS=153.003;HRun=5;HaplotypeScore=5.2587;InbreedingCoeff=-0.1585;MQ=51.66;MQ0=0;MQRankSum=-11.759;QD=0.46;ReadPosRankSum=1.329;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E319G|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E331G|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E371G|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379409|9/15|benign(0.005)|tolerated(0.28)|371/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379407|10/15|benign(0.001)|tolerated(0.21)|331/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379410|10/16|benign(0.003)|tolerated(0.26)|319/611|protein_coding|1
chr1	907774	.	G	A	268.81	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.645;DP=1416;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8695;InbreedingCoeff=-0.0177;MQ=51.53;MQ0=0;MQRankSum=0.725;QD=7.47;ReadPosRankSum=-2.464;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L324|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L336|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L376|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379409|9/15|||376/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379407|10/15|||336/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379410|10/16|||324/611|protein_coding|1
chr1	907816	.	A	G	331.68	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.634;DP=1030;Dels=0.00;FS=2.656;HRun=0;HaplotypeScore=0.8456;InbreedingCoeff=-0.0346;MQ=55.40;MQ0=0;MQRankSum=0.355;QD=10.05;ReadPosRankSum=3.222;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907920	.	C	G	216.19	.	AC=4;AF=0.0377;AN=106;BaseQRankSum=0.780;DP=253;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.2690;InbreedingCoeff=0.1203;MQ=58.25;MQ0=0;MQRankSum=-0.123;QD=16.63;ReadPosRankSum=-0.212;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907991	.	CA	C	106.79	.	AC=5;AF=0.054;AN=92;BaseQRankSum=4.179;DP=101;FS=1.708;HRun=7;HaplotypeScore=8.2099;InbreedingCoeff=0.0500;MQ=56.72;MQ0=0;MQRankSum=-1.342;QD=11.87;ReadPosRankSum=1.095;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907994	.	A	C	162.44	.	AC=5;AF=0.054;AN=92;BaseQRankSum=3.562;DP=99;Dels=0.00;FS=3.801;HRun=0;HaplotypeScore=0.0865;InbreedingCoeff=0.0684;MQ=56.41;MQ0=0;MQRankSum=-2.224;QD=16.24;ReadPosRankSum=1.331;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	907998	.	A	T	165.43	.	AC=5;AF=0.053;AN=94;BaseQRankSum=2.279;DP=96;Dels=0.00;FS=1.648;HRun=2;HaplotypeScore=0.0847;InbreedingCoeff=0.0537;MQ=56.29;MQ0=0;MQRankSum=-1.944;QD=18.38;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	908170	.	C	G	938.77	.	AC=9;AF=0.0763;AN=118;BaseQRankSum=-2.147;DP=536;Dels=0.00;FS=1.531;HRun=2;HaplotypeScore=0.5568;InbreedingCoeff=0.1081;MQ=53.86;MQ0=0;MQRankSum=0.079;QD=11.31;ReadPosRankSum=0.858;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	908228	.	A	G	406.65	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.194;DP=1035;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5043;InbreedingCoeff=-0.0201;MQ=55.14;MQ0=0;MQRankSum=1.782;QD=12.32;ReadPosRankSum=-0.055;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	908275	.	G	A	810.31	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=0.050;DP=1417;Dels=0.00;FS=4.591;HRun=0;HaplotypeScore=0.6695;InbreedingCoeff=-0.0308;MQ=55.19;MQ0=0;MQRankSum=1.728;QD=10.39;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G346D|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G358D|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G398D|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379409|10/15|benign(0.006)|tolerated(1)|398/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379407|11/15|benign(0.006)|tolerated(1)|358/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379410|11/16|benign(0.002)|tolerated(1)|346/611|protein_coding|1
chr1	908325	.	A	C	267.79	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=-17.215;DP=1827;Dels=0.00;FS=693.401;HRun=2;HaplotypeScore=3.2868;InbreedingCoeff=-0.1506;MQ=55.13;MQ0=0;MQRankSum=-1.642;QD=0.79;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T363P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T375P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T415P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379409|10/15|probably_damaging(0.998)|tolerated(0.08)|415/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379407|11/15|probably_damaging(0.998)|tolerated(0.09)|375/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379410|11/16|probably_damaging(0.995)|tolerated(0.11)|363/611|protein_coding|1
chr1	908414	.	C	T	3063.53	.	AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.682;DP=2413;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8594;InbreedingCoeff=-0.0636;MQ=57.64;MQ0=0;MQRankSum=2.858;QD=12.66;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|11),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|11),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|10),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	908823	.	G	A	12829.44	.	AC=23;AF=0.1917;AN=120;BaseQRankSum=-0.746;DP=2383;Dels=0.00;FS=3.440;HRun=0;HaplotypeScore=1.6658;InbreedingCoeff=-0.0220;MQ=59.01;MQ0=0;MQRankSum=0.792;QD=15.61;ReadPosRankSum=1.037;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|11),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|12),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|11),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909053	.	G	A	230.8	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.716;DP=1523;Dels=0.00;FS=1.669;HRun=1;HaplotypeScore=1.0522;InbreedingCoeff=-0.0166;MQ=59.32;MQ0=0;MQRankSum=-0.371;QD=14.43;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|1),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|12),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|13),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|12);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909073	.	C	T	14861.74	.	AC=51;AF=0.4250;AN=120;BaseQRankSum=-2.886;DP=1297;Dels=0.00;FS=1.649;HRun=1;HaplotypeScore=0.9560;InbreedingCoeff=-0.2187;MQ=59.41;MQ0=0;MQRankSum=-0.581;QD=17.08;ReadPosRankSum=-1.066;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|1),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|12),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|13),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|12);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909221	.	T	C	1120.5	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-0.121;DP=1389;Dels=0.00;FS=9.505;HRun=0;HaplotypeScore=0.7261;InbreedingCoeff=-0.0453;MQ=58.91;MQ0=0;MQRankSum=0.284;QD=11.55;ReadPosRankSum=3.442;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S446|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S46|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S481|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S533|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||46/176|protein_coding|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||533/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||446/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||481/611|protein_coding|1
chr1	909222	.	G	A	252.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.084;DP=1392;Dels=0.00;FS=1.211;HRun=0;HaplotypeScore=0.7091;InbreedingCoeff=-0.0090;MQ=58.92;MQ0=0;MQRankSum=0.700;QD=9.71;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A447T|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A47T|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A482T|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A534T|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0.273)|tolerated(0.13)|47/176|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0.273)|tolerated(0.47)|534/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0.273)|tolerated(0.34)|447/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0.273)|tolerated(0.48)|482/611|protein_coding|1
chr1	909238	.	G	C	30583.03	.	AC=81;AF=0.6750;AN=120;BaseQRankSum=0.003;DP=1510;Dels=0.00;FS=15.547;HRun=1;HaplotypeScore=2.2700;InbreedingCoeff=-0.0333;MQ=58.99;MQ0=0;MQRankSum=-0.442;QD=22.47;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R452P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R487P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R52P|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R539P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0)|tolerated(0.17)|52/176|protein_coding|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0)|tolerated(0.25)|539/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0)|tolerated(0.23)|452/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0)|tolerated(0.23)|487/611|protein_coding|1
chr1	909242	.	A	G	1739.34	.	AC=6;AF=0.0500;AN=120;BaseQRankSum=1.162;DP=1524;Dels=0.00;FS=7.264;HRun=2;HaplotypeScore=2.2302;InbreedingCoeff=-0.0532;MQ=58.97;MQ0=0;MQRankSum=0.469;QD=11.75;ReadPosRankSum=2.640;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G453|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G488|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G53|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G540|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||53/176|protein_coding|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||540/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||453/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||488/611|protein_coding|1
chr1	909309	.	T	C	7707.57	.	AC=26;AF=0.2167;AN=120;BaseQRankSum=5.567;DP=1519;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.7523;InbreedingCoeff=-0.0786;MQ=58.79;MQ0=0;MQRankSum=1.234;QD=13.69;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S476P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S511P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S563P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S76P|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0.013)|tolerated(0.25)|76/176|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0.013)|tolerated(0.3)|563/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0)|tolerated(0.3)|476/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0.02)|tolerated(0.29)|511/611|protein_coding|1
chr1	909320	.	C	T	232.62	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.426;DP=1387;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8928;InbreedingCoeff=-0.0090;MQ=58.83;MQ0=0;MQRankSum=0.287;QD=10.57;ReadPosRankSum=2.476;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P479|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P514|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P566|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P79|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||79/176|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||566/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||479/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||514/611|protein_coding|1
chr1	909326	.	C	T	373.87	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.393;DP=1276;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8069;InbreedingCoeff=-0.0180;MQ=58.80;MQ0=0;MQRankSum=0.099;QD=8.90;ReadPosRankSum=1.847;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G481|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G516|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G568|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G81|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||81/176|protein_coding|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||568/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||481/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||516/611|protein_coding|1
chr1	909363	.	A	C	203.29	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.679;DP=1010;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.5429;InbreedingCoeff=-0.0117;MQ=59.04;MQ0=0;MQRankSum=0.409;QD=11.29;ReadPosRankSum=2.880;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R494|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R529|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R581|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R94|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||94/176|protein_coding|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||581/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||494/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||529/611|protein_coding|1
chr1	909419	.	C	T	1837.1	.	AC=16;AF=0.1333;AN=120;BaseQRankSum=-3.072;DP=694;Dels=0.00;FS=2.424;HRun=0;HaplotypeScore=0.2284;InbreedingCoeff=-0.0370;MQ=58.46;MQ0=0;MQRankSum=0.397;QD=12.17;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D112|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D512|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D547|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D599|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||112/176|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||599/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||512/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||547/611|protein_coding|1
chr1	909523	.	G	A	539.82	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.755;DP=1030;Dels=0.00;FS=12.426;HRun=1;HaplotypeScore=0.5627;InbreedingCoeff=-0.0151;MQ=58.16;MQ0=0;MQRankSum=0.665;QD=10.80;ReadPosRankSum=0.177;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909554	.	CA	C	2082.11	.	AC=48;AF=0.4000;AN=120;BaseQRankSum=7.755;DP=1646;FS=15.954;HRun=1;HaplotypeScore=179.7893;InbreedingCoeff=-0.1499;MQ=58.00;MQ0=0;MQRankSum=2.728;QD=1.74;ReadPosRankSum=-12.687;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909555	.	A	G	55343.84	.	AC=113;AF=0.9417;AN=120;BaseQRankSum=2.487;DP=1646;Dels=0.01;FS=6.244;HRun=6;HaplotypeScore=1.1341;InbreedingCoeff=-0.0625;MQ=58.00;MQ0=0;MQRankSum=0.381;QD=33.62;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909768	.	A	G	183199.18	.	AC=120;AF=1.0000;AN=120;BaseQRankSum=0.728;DP=5372;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=2.6976;InbreedingCoeff=-0.0000;MQ=58.76;MQ0=0;MQRankSum=2.388;QD=34.10;ReadPosRankSum=1.847;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|14),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|15),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|14);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1
chr1	909960	.	C	T	318.47	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.416;DP=1592;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.2673;InbreedingCoeff=-0.0090;MQ=58.66;MQ0=0;MQRankSum=-0.101;QD=11.80;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),UTR_3_PRIME(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16),UTR_3_PRIME(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|15);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000491024|4/5|||-/176|protein_coding|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379409|15/15|||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379407|15/15|||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1
chr1	910394	.	C	T	398.09	.	AC=13;AF=0.361;AN=36;BaseQRankSum=1.775;DP=46;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0554;InbreedingCoeff=0.3755;MQ=58.99;MQ0=0;MQRankSum=0.823;QD=23.42;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1
chr1	910438	.	A	G	1374.53	.	AC=42;AF=1.000;AN=42;DP=42;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1458;MQ=57.77;MQ0=0;QD=33.53;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1
chr1	910473	.	G	A	299.74	.	AC=11;AF=0.250;AN=44;BaseQRankSum=-1.316;DP=64;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.1771;MQ=59.28;MQ0=0;MQRankSum=0.212;QD=12.49;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1
chr1	934099	.	G	C	525.65	.	AC=24;AF=1.000;AN=24;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1752;MQ=57.23;MQ0=0;QD=30.92;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	934106	.	A	G	492.03	.	AC=22;AF=1.000;AN=22;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1738;MQ=57.23;MQ0=0;QD=30.75;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	934130	.	G	C	64.94	.	AC=4;AF=0.222;AN=18;BaseQRankSum=-0.306;DP=15;Dels=0.00;FS=2.515;HRun=0;HaplotypeScore=0.2219;MQ=56.85;MQ0=0;MQRankSum=-0.551;QD=12.99;ReadPosRankSum=2.388;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	934797	.	T	G	52.82	.	AC=6;AF=0.067;AN=90;BaseQRankSum=-1.481;DP=224;Dels=0.00;FS=43.747;HRun=4;HaplotypeScore=0.0853;InbreedingCoeff=-0.0492;MQ=49.44;MQ0=0;MQRankSum=-1.914;QD=1.51;ReadPosRankSum=0.524;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D103A|221|HES4|protein_coding|CODING|ENST00000304952|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D129A|247|HES4|protein_coding|CODING|ENST00000428771|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D71A|189|HES4|protein_coding|CODING|ENST00000484667|);CSQ=missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000484667|3/3|probably_damaging(0.994)|deleterious(0)|71/189|protein_coding|1,missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000428771|3/3|benign(0.358)|deleterious(0)|129/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|2/2||||retained_intron|1,missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000304952|4/4|probably_damaging(0.979)|deleterious(0)|103/221|protein_coding|1
chr1	934888	.	C	A	233.29	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.550;DP=738;Dels=0.00;FS=2.017;HRun=0;HaplotypeScore=1.1956;InbreedingCoeff=-0.0253;MQ=56.42;MQ0=0;MQRankSum=-0.145;QD=7.07;ReadPosRankSum=-0.918;EFF=INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|2),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|3),INTRON(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|2),INTRON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,intron_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	934990	.	A	G	108.0	.	AC=12;AF=0.1017;AN=118;BaseQRankSum=-13.261;DP=1923;Dels=0.00;FS=97.152;HRun=3;HaplotypeScore=3.2884;InbreedingCoeff=-0.1051;MQ=46.21;MQ0=0;MQRankSum=-9.305;QD=0.35;ReadPosRankSum=0.938;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S38P|189|HES4|protein_coding|CODING|ENST00000484667|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S70P|221|HES4|protein_coding|CODING|ENST00000304952|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S96P|247|HES4|protein_coding|CODING|ENST00000428771|);CSQ=missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000484667|2/3|probably_damaging(0.979)|deleterious(0)|38/189|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000428771|2/3|benign(0.444)|deleterious(0.02)|96/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000304952|3/4|possibly_damaging(0.534)|deleterious(0.01)|70/221|protein_coding|1
chr1	935046	.	G	A	2684.85	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.713;DP=2876;Dels=0.00;FS=0.372;HRun=0;HaplotypeScore=3.4737;InbreedingCoeff=-0.0181;MQ=51.17;MQ0=0;MQRankSum=0.144;QD=11.88;ReadPosRankSum=0.789;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|1),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|2),INTRON(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|1);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,intron_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	935222	.	C	A	15396.75	.	AC=74;AF=0.6167;AN=120;BaseQRankSum=-9.471;DP=941;Dels=0.00;FS=3.802;HRun=0;HaplotypeScore=1.0918;InbreedingCoeff=-0.0313;MQ=53.20;MQ0=0;MQRankSum=2.504;QD=20.02;ReadPosRankSum=1.296;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|1),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R44S|247|HES4|protein_coding|CODING|ENST00000428771|);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,missense_variant|agG/agT|R/S|ENSG00000188290|HES4|ENST00000428771|1/3|benign(0)|tolerated(0.95)|44/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	935459	.	A	G	44.02	.	AC=4;AF=0.67;AN=6;BaseQRankSum=-0.736;DP=4;Dels=0.00;FS=4.771;HRun=2;HaplotypeScore=0.0000;MQ=47.12;MQ0=0;MQRankSum=0.736;QD=22.01;ReadPosRankSum=0.736;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UTR_5_PRIME(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|1),UTR_5_PRIME(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|1);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000428771|1/3|||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000304952|1/4|||-/221|protein_coding|1
chr1	935492	.	G	T	38.54	.	AC=4;AF=0.50;AN=8;BaseQRankSum=1.026;DP=5;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.2167;MQ=49.96;MQ0=0;MQRankSum=1.026;QD=19.27;ReadPosRankSum=-1.026;EFF=START_GAINED(LOW||||247|HES4|protein_coding|CODING|ENST00000428771|1),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000428771|1/3|||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	935715	.	C	T	119.53	.	AC=6;AF=0.75;AN=8;BaseQRankSum=0.731;DP=6;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=0.731;QD=29.88;ReadPosRankSum=0.731;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	935833	.	C	G	205.67	.	AC=10;AF=1.00;AN=10;DP=7;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=56.62;MQ0=0;QD=29.38;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1
chr1	948421	.	A	AAAC	726.92	.	AC=22;AF=1.000;AN=22;DP=20;FS=0.000;HRun=0;HaplotypeScore=4.9337;InbreedingCoeff=-0.1734;MQ=46.54;MQ0=0;QD=45.43;EFF=EXON(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|1),UPSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.10|processed_pseudogene|NON_CODING|ENST00000423619|);CSQ=upstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000231702|RP11-54O7.10|ENST00000423619|||||processed_pseudogene|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000224969|RP11-54O7.11|ENST00000458555|1/2||||antisense|1
chr1	948692	.	G	A	6273.5	.	AC=98;AF=0.8909;AN=110;BaseQRankSum=0.890;DP=195;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1286;InbreedingCoeff=0.1904;MQ=57.72;MQ0=0;MQRankSum=0.244;QD=33.91;ReadPosRankSum=-0.202;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=upstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948844	.	C	CT	12812.2	.	AC=110;AF=0.9167;AN=120;BaseQRankSum=12.848;DP=1613;FS=0.638;HRun=2;HaplotypeScore=267.6122;InbreedingCoeff=0.3293;MQ=57.07;MQ0=0;MQRankSum=-0.300;QD=8.17;ReadPosRankSum=0.729;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant&feature_elongation|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948846	.	T	A	156.11	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=-3.754;DP=1643;Dels=0.00;FS=73.746;HRun=1;HaplotypeScore=23.6593;InbreedingCoeff=-0.0805;MQ=57.11;MQ0=0;MQRankSum=1.518;QD=0.75;ReadPosRankSum=-12.345;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948846	.	T	TA	63344.05	.	AC=112;AF=0.9333;AN=120;BaseQRankSum=7.480;DP=1716;FS=0.000;HRun=1;HaplotypeScore=206.0209;InbreedingCoeff=-0.0721;MQ=56.50;MQ0=0;MQRankSum=0.146;QD=36.91;ReadPosRankSum=-0.823;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant&feature_elongation|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948869	.	C	T	230.26	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.821;DP=2138;Dels=0.00;FS=1.991;HRun=0;HaplotypeScore=1.4232;InbreedingCoeff=-0.0088;MQ=56.52;MQ0=0;MQRankSum=2.379;QD=11.51;ReadPosRankSum=-0.420;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948870	.	C	G	69163.2	.	AC=112;AF=0.9333;AN=120;BaseQRankSum=0.502;DP=2189;Dels=0.00;FS=1.037;HRun=1;HaplotypeScore=1.4157;InbreedingCoeff=-0.0719;MQ=56.60;MQ0=0;MQRankSum=-0.899;QD=31.60;ReadPosRankSum=-1.945;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	948921	.	T	C	105377.26	.	AC=112;AF=0.9333;AN=120;BaseQRankSum=0.554;DP=3568;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.5426;InbreedingCoeff=-0.0712;MQ=57.76;MQ0=0;MQRankSum=-1.329;QD=29.53;ReadPosRankSum=-3.423;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949053	.	C	G	1016.17	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.017;DP=2444;Dels=0.00;FS=9.350;HRun=2;HaplotypeScore=1.7725;InbreedingCoeff=0.6430;MQ=57.83;MQ0=0;MQRankSum=-0.809;QD=17.22;ReadPosRankSum=0.511;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949123	.	G	A	102.54	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.767;DP=1126;Dels=0.00;FS=2.226;HRun=0;HaplotypeScore=0.7464;InbreedingCoeff=-0.0173;MQ=58.11;MQ0=0;MQRankSum=0.187;QD=6.03;ReadPosRankSum=-1.626;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949235	.	G	A	32604.9	.	AC=112;AF=0.9333;AN=120;BaseQRankSum=-0.988;DP=993;Dels=0.00;FS=7.691;HRun=0;HaplotypeScore=0.4657;InbreedingCoeff=-0.0787;MQ=58.29;MQ0=0;MQRankSum=-1.787;QD=32.83;ReadPosRankSum=-1.094;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949302	.	G	A	113.2	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.449;DP=1914;Dels=0.00;FS=2.069;HRun=0;HaplotypeScore=1.3393;InbreedingCoeff=-0.0087;MQ=58.25;MQ0=0;MQRankSum=1.862;QD=8.71;ReadPosRankSum=1.655;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949422	.	G	A	479.41	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.293;DP=3045;Dels=0.00;FS=6.680;HRun=1;HaplotypeScore=1.7335;InbreedingCoeff=-0.0084;MQ=58.77;MQ0=0;MQRankSum=-1.068;QD=12.29;ReadPosRankSum=-1.019;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S21N|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|aGc/aAc|S/N|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0)|tolerated(0.74)|21/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949608	.	G	A	34851.76	.	AC=42;AF=0.3500;AN=120;BaseQRankSum=0.005;DP=2776;Dels=0.00;FS=11.466;HRun=1;HaplotypeScore=1.6893;InbreedingCoeff=-0.0991;MQ=58.46;MQ0=0;MQRankSum=1.157;QD=19.90;ReadPosRankSum=1.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S83N|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|aGc/aAc|S/N|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.002)|tolerated(0.25)|83/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949654	.	A	G	103598.95	.	AC=108;AF=0.9000;AN=120;BaseQRankSum=3.046;DP=3818;Dels=0.00;FS=9.083;HRun=0;HaplotypeScore=2.1911;InbreedingCoeff=0.0821;MQ=58.12;MQ0=0;MQRankSum=-0.993;QD=27.83;ReadPosRankSum=-2.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V98|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=synonymous_variant|gtA/gtG|V|ENSG00000187608|ISG15|ENST00000379389|2/2|||98/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949655	.	C	T	133.5	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.364;DP=3843;Dels=0.00;FS=4.847;HRun=0;HaplotypeScore=2.2366;InbreedingCoeff=-0.0167;MQ=58.08;MQ0=0;MQRankSum=1.217;QD=2.97;ReadPosRankSum=-1.553;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R99W|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.007)|tolerated(0.2)|99/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949831	.	C	T	3120.79	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.506;DP=2204;Dels=0.00;FS=25.676;HRun=0;HaplotypeScore=2.0744;InbreedingCoeff=-0.0327;MQ=57.33;MQ0=0;MQRankSum=-0.396;QD=12.43;ReadPosRankSum=2.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G157|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=synonymous_variant|ggC/ggT|G|ENSG00000187608|ISG15|ENST00000379389|2/2|||157/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949832	.	G	A	1258.11	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.608;DP=2177;Dels=0.00;FS=0.646;HRun=0;HaplotypeScore=2.0191;InbreedingCoeff=-0.0169;MQ=57.31;MQ0=0;MQRankSum=2.168;QD=12.21;ReadPosRankSum=-0.092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G158S|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.009)|tolerated(0.54)|158/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949884	.	A	C	542.9	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=0.716;DP=1463;Dels=0.00;FS=4.086;HRun=0;HaplotypeScore=1.0630;InbreedingCoeff=-0.0204;MQ=58.08;MQ0=0;MQRankSum=-0.256;QD=14.67;ReadPosRankSum=3.251;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_3_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|2);CSQ=3_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|2/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949889	.	G	A	1254.48	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.111;DP=1383;Dels=0.00;FS=3.846;HRun=2;HaplotypeScore=1.0736;InbreedingCoeff=-0.0309;MQ=58.18;MQ0=0;MQRankSum=-0.749;QD=12.93;ReadPosRankSum=2.198;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_3_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|2);CSQ=3_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|2/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	949925	.	C	T	25659.52	.	AC=103;AF=0.8879;AN=116;BaseQRankSum=0.388;DP=769;Dels=0.00;FS=1.403;HRun=0;HaplotypeScore=0.4309;InbreedingCoeff=0.1833;MQ=58.18;MQ0=0;MQRankSum=0.782;QD=33.54;ReadPosRankSum=-1.626;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	950113	.	GAAGT	G	1437.6	.	AC=33;AF=0.532;AN=62;BaseQRankSum=4.162;DP=62;FS=0.000;HRun=0;HaplotypeScore=9.8036;InbreedingCoeff=0.1341;MQ=49.27;MQ0=0;MQRankSum=-5.026;QD=34.23;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	950243	.	A	C	341.55	.	AC=21;AF=0.553;AN=38;BaseQRankSum=1.286;DP=25;Dels=0.00;FS=2.282;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.2744;MQ=57.17;MQ0=0;MQRankSum=1.615;QD=24.40;ReadPosRankSum=0.099;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1
chr1	955016	.	A	G	41.68	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=47.12;MQ0=0;QD=20.84;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	955213	.	T	C	205.28	.	AC=12;AF=1.000;AN=12;DP=7;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=49.17;MQ0=0;QD=29.33;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	955597	.	G	T	397.16	.	AC=19;AF=0.339;AN=56;BaseQRankSum=-2.859;DP=48;Dels=0.00;FS=4.867;HRun=0;HaplotypeScore=0.0297;InbreedingCoeff=0.3749;MQ=53.41;MQ0=0;MQRankSum=0.000;QD=22.06;ReadPosRankSum=2.226;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P15|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|ccG/ccT|P|ENSG00000188157|AGRN|ENST00000379370|1/36|||15/2045|protein_coding|1
chr1	956061	.	A	AG	112.73	.	AC=10;AF=0.556;AN=18;BaseQRankSum=0.851;DP=13;FS=0.000;HRun=7;HaplotypeScore=6.0534;MQ=48.24;MQ0=0;MQRankSum=-1.268;QD=22.55;ReadPosRankSum=0.103;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	956077	.	C	T	53.71	.	AC=5;AF=0.250;AN=20;BaseQRankSum=1.109;DP=15;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1223;MQ=51.77;MQ0=0;MQRankSum=0.370;QD=13.43;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957120	.	G	C	112.86	.	AC=7;AF=0.250;AN=28;BaseQRankSum=-0.158;DP=18;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0000;InbreedingCoeff=0.1430;MQ=57.39;MQ0=0;MQRankSum=-0.791;QD=18.81;ReadPosRankSum=0.791;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957474	.	C	G	88.48	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.393;DP=913;Dels=0.00;FS=13.654;HRun=0;HaplotypeScore=0.3942;InbreedingCoeff=-0.0138;MQ=58.75;MQ0=0;MQRankSum=0.079;QD=4.02;ReadPosRankSum=2.320;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957568	.	A	G	559.04	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.476;DP=2810;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8451;InbreedingCoeff=-0.0085;MQ=58.63;MQ0=0;MQRankSum=0.035;QD=11.41;ReadPosRankSum=2.360;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957640	.	C	T	832.22	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.040;DP=3915;Dels=0.00;FS=3.301;HRun=0;HaplotypeScore=2.0922;InbreedingCoeff=-0.0143;MQ=58.81;MQ0=0;MQRankSum=0.961;QD=12.06;ReadPosRankSum=1.475;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D87|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|gaC/gaT|D|ENSG00000188157|AGRN|ENST00000379370|2/36|||87/2045|protein_coding|1
chr1	957667	.	C	T	1421.68	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-3.679;DP=4208;Dels=0.00;FS=3.179;HRun=3;HaplotypeScore=2.6513;InbreedingCoeff=-0.0085;MQ=58.87;MQ0=0;MQRankSum=-0.384;QD=13.94;ReadPosRankSum=1.504;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G96|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|ggC/ggT|G|ENSG00000188157|AGRN|ENST00000379370|2/36|||96/2045|protein_coding|1
chr1	957898	.	G	T	11511.79	.	AC=35;AF=0.2917;AN=120;BaseQRankSum=-2.213;DP=1017;Dels=0.00;FS=12.996;HRun=0;HaplotypeScore=0.9917;InbreedingCoeff=-0.0796;MQ=55.78;MQ0=0;MQRankSum=2.025;QD=19.92;ReadPosRankSum=0.609;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957967	.	T	TTGTAGTCTGACCTGTGGTCTGAC	98446.19	.	AC=111;AF=0.9737;AN=114;BaseQRankSum=-1.879;DP=448;FS=0.000;HRun=0;HaplotypeScore=117.9611;InbreedingCoeff=-0.0725;MQ=36.18;MQ0=0;MQRankSum=-4.523;QD=220.24;ReadPosRankSum=-0.243;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957971	.	G	A	6538.45	.	AC=64;AF=0.5614;AN=114;BaseQRankSum=3.096;DP=423;Dels=0.00;FS=0.554;HRun=0;HaplotypeScore=1.4918;InbreedingCoeff=-0.6704;MQ=34.45;MQ0=0;MQRankSum=-1.012;QD=15.60;ReadPosRankSum=0.359;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957975	.	C	T	5244.2	.	AC=61;AF=0.5446;AN=112;BaseQRankSum=3.205;DP=388;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4483;InbreedingCoeff=-0.7134;MQ=33.55;MQ0=0;MQRankSum=-2.362;QD=13.66;ReadPosRankSum=-15.499;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	957976	.	A	G	4910.47	.	AC=60;AF=0.5455;AN=110;BaseQRankSum=4.309;DP=381;Dels=0.00;FS=1.187;HRun=0;HaplotypeScore=1.4201;InbreedingCoeff=-0.7088;MQ=32.86;MQ0=0;MQRankSum=-2.293;QD=13.03;ReadPosRankSum=-15.805;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	958204	.	C	A	854.8	.	AC=2;AF=0.025;AN=80;BaseQRankSum=1.546;DP=704;Dels=0.00;FS=3.962;HRun=1;HaplotypeScore=0.3471;InbreedingCoeff=-0.0900;MQ=57.09;MQ0=0;MQRankSum=0.211;QD=16.13;ReadPosRankSum=1.802;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	958236	.	T	C	367.45	.	AC=1;AF=0.013;AN=76;BaseQRankSum=-0.984;DP=1202;Dels=0.00;FS=6.974;HRun=2;HaplotypeScore=0.8541;InbreedingCoeff=-0.0759;MQ=56.81;MQ0=0;MQRankSum=0.871;QD=11.85;ReadPosRankSum=-0.134;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	958248	.	A	G	14600.85	.	AC=22;AF=0.297;AN=74;BaseQRankSum=6.262;DP=1397;Dels=0.00;FS=8.143;HRun=2;HaplotypeScore=1.8858;InbreedingCoeff=0.1339;MQ=57.01;MQ0=0;MQRankSum=0.270;QD=19.06;ReadPosRankSum=0.054;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1
chr1	970215	.	G	C	1422.62	.	AC=29;AF=0.483;AN=60;BaseQRankSum=-0.953;DP=94;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0644;InbreedingCoeff=0.4677;MQ=55.42;MQ0=0;MQRankSum=2.956;QD=30.27;ReadPosRankSum=1.616;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970549	.	TGG	T	8449.83	.	AC=65;AF=0.5603;AN=116;BaseQRankSum=-6.256;DP=1747;FS=120.761;HRun=13;HaplotypeScore=284.3804;InbreedingCoeff=-0.5216;MQ=44.59;MQ0=0;MQRankSum=0.141;QD=5.09;ReadPosRankSum=4.437;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970559	.	GGGGT	G	251.0	.	AC=12;AF=0.1017;AN=118;BaseQRankSum=-0.439;DP=2064;FS=2.290;HRun=0;HaplotypeScore=346.6420;InbreedingCoeff=-0.1291;MQ=46.51;MQ0=0;MQRankSum=-12.374;QD=0.60;ReadPosRankSum=6.900;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970560	.	GGGT	G	6238.85	.	AC=51;AF=0.4322;AN=118;BaseQRankSum=10.237;DP=2102;FS=59.155;HRun=0;HaplotypeScore=328.0111;InbreedingCoeff=-0.7958;MQ=46.78;MQ0=0;MQRankSum=-6.210;QD=3.10;ReadPosRankSum=17.494;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970561	.	GGT	G	13756.94	.	AC=57;AF=0.4831;AN=118;BaseQRankSum=18.075;DP=2129;FS=78.149;HRun=0;HaplotypeScore=306.3538;InbreedingCoeff=-0.8937;MQ=47.00;MQ0=0;MQRankSum=-8.327;QD=6.50;ReadPosRankSum=23.377;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970562	.	GT	G	11726.17	.	AC=56;AF=0.4746;AN=118;BaseQRankSum=20.100;DP=2148;FS=44.156;HRun=1;HaplotypeScore=301.2279;InbreedingCoeff=-0.8639;MQ=47.47;MQ0=0;MQRankSum=-8.868;QD=5.54;ReadPosRankSum=21.869;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970573	.	T	G	1645.49	.	AC=31;AF=0.2583;AN=120;BaseQRankSum=-22.121;DP=2678;Dels=0.00;FS=172.614;HRun=4;HaplotypeScore=23.1118;InbreedingCoeff=-0.3662;MQ=49.95;MQ0=0;MQRankSum=-11.517;QD=1.06;ReadPosRankSum=19.788;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970765	.	C	T	1353.46	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.165;DP=4536;Dels=0.00;FS=22.500;HRun=0;HaplotypeScore=2.7925;InbreedingCoeff=-0.0084;MQ=57.72;MQ0=0;MQRankSum=1.115;QD=12.65;ReadPosRankSum=3.005;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970836	.	G	A	214.73	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.962;DP=2105;Dels=0.00;FS=7.794;HRun=0;HaplotypeScore=1.1718;InbreedingCoeff=-0.0084;MQ=57.64;MQ0=0;MQRankSum=0.008;QD=10.74;ReadPosRankSum=1.304;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	970915	.	C	T	377.1	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=2.244;DP=644;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3824;InbreedingCoeff=-0.0289;MQ=57.36;MQ0=0;MQRankSum=0.823;QD=9.20;ReadPosRankSum=1.968;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	971224	.	A	G	877.98	.	AC=35;AF=0.921;AN=38;BaseQRankSum=0.367;DP=38;Dels=0.00;FS=6.105;HRun=6;HaplotypeScore=0.1297;InbreedingCoeff=0.0071;MQ=58.78;MQ0=0;MQRankSum=0.367;QD=27.44;ReadPosRankSum=0.768;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	975702	.	A	G	736.88	.	AC=30;AF=0.833;AN=36;BaseQRankSum=1.380;DP=25;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0438;InbreedingCoeff=0.2327;MQ=57.17;MQ0=0;MQRankSum=0.794;QD=33.49;ReadPosRankSum=-0.544;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	976428	.	C	A	86.19	.	AC=8;AF=1.00;AN=8;DP=10;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5990;MQ=29.00;MQ0=0;QD=21.55;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|4),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|2),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	976514	.	C	A	153.87	.	AC=10;AF=0.833;AN=12;BaseQRankSum=0.742;DP=14;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=40.36;MQ0=0;MQRankSum=-0.742;QD=25.65;ReadPosRankSum=-0.742;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|4),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|2),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977203	.	G	C	14246.35	.	AC=102;AF=0.8947;AN=114;BaseQRankSum=0.075;DP=497;Dels=0.00;FS=12.091;HRun=1;HaplotypeScore=0.3092;InbreedingCoeff=0.1183;MQ=53.27;MQ0=0;MQRankSum=-0.225;QD=29.99;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977220	.	C	T	77.62	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.664;DP=734;Dels=0.00;FS=6.335;HRun=1;HaplotypeScore=0.5865;InbreedingCoeff=-0.0433;MQ=54.41;MQ0=0;MQRankSum=-0.052;QD=3.53;ReadPosRankSum=0.239;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977294	.	G	A	323.25	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.012;DP=2064;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.9641;InbreedingCoeff=-0.0130;MQ=55.98;MQ0=0;MQRankSum=1.642;QD=9.51;ReadPosRankSum=0.377;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977330	.	T	C	75130.94	.	AC=107;AF=0.8917;AN=120;BaseQRankSum=4.114;DP=2805;Dels=0.00;FS=1.138;HRun=2;HaplotypeScore=2.7705;InbreedingCoeff=0.2224;MQ=56.35;MQ0=0;MQRankSum=1.859;QD=27.97;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977356	.	C	T	37.67	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.314;DP=3180;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.0624;InbreedingCoeff=-0.0085;MQ=56.04;MQ0=0;MQRankSum=1.209;QD=3.42;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R400W|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000188157|AGRN|ENST00000379370|7/36|benign(0.061)|deleterious(0.02)|400/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977570	.	G	A	23442.1	.	AC=102;AF=0.8500;AN=120;BaseQRankSum=-2.570;DP=882;Dels=0.00;FS=3.065;HRun=0;HaplotypeScore=1.0563;InbreedingCoeff=0.1840;MQ=56.97;MQ0=0;MQRankSum=1.250;QD=27.84;ReadPosRankSum=-0.551;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	977780	.	C	T	1896.26	.	AC=55;AF=0.833;AN=66;BaseQRankSum=-0.091;DP=70;Dels=0.00;FS=1.840;HRun=0;HaplotypeScore=0.0570;InbreedingCoeff=0.2412;MQ=56.97;MQ0=0;MQRankSum=0.071;QD=30.10;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978183	.	C	G	34.17	.	AC=2;AF=0.043;AN=46;BaseQRankSum=1.339;DP=53;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0869;InbreedingCoeff=0.1027;MQ=58.24;MQ0=0;MQRankSum=1.491;QD=17.09;ReadPosRankSum=0.025;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978193	.	G	A	202.48	.	AC=6;AF=0.125;AN=48;BaseQRankSum=0.284;DP=51;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0833;InbreedingCoeff=-0.1181;MQ=58.63;MQ0=0;MQRankSum=-0.041;QD=14.46;ReadPosRankSum=0.527;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978576	.	A	AG	514.05	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.254;DP=2624;FS=0.000;HRun=7;HaplotypeScore=255.5270;InbreedingCoeff=-0.0227;MQ=57.44;MQ0=0;MQRankSum=-3.300;QD=9.70;ReadPosRankSum=-2.347;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978600	.	GCC	G	17413.56	.	AC=61;AF=0.5169;AN=118;BaseQRankSum=43.323;DP=3497;FS=2.177;HRun=4;HaplotypeScore=348.2579;InbreedingCoeff=-0.1331;MQ=57.63;MQ0=0;MQRankSum=3.380;QD=6.27;ReadPosRankSum=3.269;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978603	.	CCT	C	71936.99	.	AC=63;AF=0.5339;AN=118;BaseQRankSum=27.120;DP=3635;FS=0.415;HRun=0;HaplotypeScore=268.7446;InbreedingCoeff=-0.1355;MQ=57.70;MQ0=0;MQRankSum=-0.052;QD=24.97;ReadPosRankSum=2.237;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978604	.	CTG	C	22255.35	.	AC=63;AF=0.5339;AN=118;BaseQRankSum=42.643;DP=3702;FS=4.247;HRun=0;HaplotypeScore=358.4425;InbreedingCoeff=-0.1343;MQ=57.72;MQ0=0;MQRankSum=2.535;QD=7.58;ReadPosRankSum=3.410;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978762	.	G	A	3088.0	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.970;DP=3629;Dels=0.00;FS=0.380;HRun=0;HaplotypeScore=2.3356;InbreedingCoeff=-0.0359;MQ=57.56;MQ0=0;MQRankSum=1.561;QD=14.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G510S|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Ggc/Agc|G/S|ENSG00000188157|AGRN|ENST00000379370|8/36|probably_damaging(0.961)|tolerated(0.05)|510/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978850	.	T	G	355.87	.	AC=13;AF=0.1083;AN=120;BaseQRankSum=-20.130;DP=2142;Dels=0.00;FS=811.949;HRun=3;HaplotypeScore=4.6408;InbreedingCoeff=-0.1393;MQ=53.60;MQ0=0;MQRankSum=-8.269;QD=0.90;ReadPosRankSum=-1.238;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|8),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	978857	.	T	G	60.53	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=-18.263;DP=2025;Dels=0.01;FS=633.354;HRun=4;HaplotypeScore=4.9061;InbreedingCoeff=-0.0867;MQ=53.43;MQ0=0;MQRankSum=-5.927;QD=0.18;ReadPosRankSum=3.709;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|8),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979594	.	C	T	694.16	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.081;DP=5875;DS;Dels=0.00;FS=21.795;HRun=0;HaplotypeScore=3.6311;InbreedingCoeff=-0.0090;MQ=57.97;MQ0=0;MQRankSum=1.076;QD=13.10;ReadPosRankSum=-2.987;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P702L|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000188157|AGRN|ENST00000379370|11/36|probably_damaging(0.931)|tolerated(0.29)|702/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979669	.	G	A	1676.8	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-2.241;DP=3939;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.9042;InbreedingCoeff=-0.0141;MQ=56.95;MQ0=0;MQRankSum=-0.084;QD=10.10;ReadPosRankSum=1.062;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|11),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979690	.	G	A	3048.77	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.190;DP=3529;Dels=0.00;FS=4.170;HRun=0;HaplotypeScore=1.8409;InbreedingCoeff=-0.0220;MQ=57.08;MQ0=0;MQRankSum=0.399;QD=11.82;ReadPosRankSum=-0.422;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|11),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979748	.	A	T	1423.3	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.288;DP=3261;Dels=0.00;FS=1.119;HRun=0;HaplotypeScore=1.7332;InbreedingCoeff=-0.0175;MQ=58.27;MQ0=0;MQRankSum=0.306;QD=11.21;ReadPosRankSum=1.431;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gTg|E728V|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|gAg/gTg|E/V|ENSG00000188157|AGRN|ENST00000379370|12/36|probably_damaging(0.932)|deleterious(0.02)|728/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979835	.	G	A	1973.32	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=-1.744;DP=1701;Dels=0.00;FS=1.140;HRun=0;HaplotypeScore=1.2871;InbreedingCoeff=-0.0241;MQ=58.02;MQ0=0;MQRankSum=1.712;QD=14.00;ReadPosRankSum=0.225;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	979890	.	C	T	106.44	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.494;DP=863;Dels=0.00;FS=2.607;HRun=0;HaplotypeScore=0.6567;InbreedingCoeff=-0.0292;MQ=58.16;MQ0=0;MQRankSum=-0.586;QD=9.68;ReadPosRankSum=0.909;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980077	.	C	T	58.05	.	AC=1;AF=0.012;AN=86;BaseQRankSum=-0.500;DP=105;Dels=0.00;FS=12.895;HRun=0;HaplotypeScore=0.1629;InbreedingCoeff=-0.1341;MQ=58.00;MQ0=0;MQRankSum=0.378;QD=11.61;ReadPosRankSum=0.765;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980189	.	G	A	62.31	.	AC=2;AF=0.032;AN=62;BaseQRankSum=-0.689;DP=65;Dels=0.00;FS=2.622;HRun=0;HaplotypeScore=0.0923;InbreedingCoeff=0.0483;MQ=58.57;MQ0=0;MQRankSum=-0.262;QD=20.77;ReadPosRankSum=-0.131;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980276	.	C	T	58.0	.	AC=2;AF=0.021;AN=96;BaseQRankSum=-2.227;DP=125;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1208;InbreedingCoeff=0.0215;MQ=58.51;MQ0=0;MQRankSum=0.682;QD=14.50;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980460	.	G	A	26594.59	.	AC=107;AF=0.8917;AN=120;BaseQRankSum=-2.656;DP=975;Dels=0.00;FS=0.883;HRun=0;HaplotypeScore=0.8473;InbreedingCoeff=0.2169;MQ=58.13;MQ0=0;MQRankSum=-0.492;QD=28.60;ReadPosRankSum=0.989;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980824	.	G	C	275.83	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.440;DP=1969;Dels=0.00;FS=12.667;HRun=0;HaplotypeScore=2.5993;InbreedingCoeff=-0.0094;MQ=58.48;MQ0=0;MQRankSum=1.465;QD=11.99;ReadPosRankSum=-0.443;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G819|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000188157|AGRN|ENST00000379370|14/36|||819/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|1/4||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980941	.	C	T	600.94	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.751;DP=2190;Dels=0.00;FS=4.066;HRun=0;HaplotypeScore=1.5643;InbreedingCoeff=-0.0087;MQ=58.24;MQ0=0;MQRankSum=0.449;QD=12.02;ReadPosRankSum=0.589;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980948	.	C	T	538.98	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.096;DP=2144;Dels=0.00;FS=17.669;HRun=0;HaplotypeScore=2.3599;InbreedingCoeff=-0.0087;MQ=58.24;MQ0=0;MQRankSum=-0.314;QD=17.39;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	980955	.	AC	A	1099.14	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=8.294;DP=2110;FS=28.545;HRun=5;HaplotypeScore=116.2371;InbreedingCoeff=-0.0170;MQ=58.34;MQ0=0;MQRankSum=-0.585;QD=9.16;ReadPosRankSum=1.829;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	981087	.	A	G	111674.9	.	AC=105;AF=0.8750;AN=120;BaseQRankSum=2.112;DP=3879;Dels=0.00;FS=2.321;HRun=0;HaplotypeScore=2.2416;InbreedingCoeff=0.1619;MQ=58.40;MQ0=0;MQRankSum=-0.442;QD=29.96;ReadPosRankSum=-1.459;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1
chr1	981131	.	A	G	3064.9	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.865;DP=5182;Dels=0.00;FS=11.038;HRun=0;HaplotypeScore=2.4921;InbreedingCoeff=-0.0256;MQ=58.34;MQ0=0;MQRankSum=1.546;QD=10.79;ReadPosRankSum=1.415;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q852R|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cAa/cGa|Q/R|ENSG00000188157|AGRN|ENST00000379370|15/36|benign(0.227)|tolerated(0.44)|852/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|2/4||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	981931	.	A	G	38481.37	.	AC=102;AF=0.8500;AN=120;BaseQRankSum=4.244;DP=1481;Dels=0.00;FS=5.461;HRun=0;HaplotypeScore=0.5832;InbreedingCoeff=0.0829;MQ=57.68;MQ0=0;MQRankSum=2.481;QD=26.85;ReadPosRankSum=-2.762;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1022|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|tcA/tcG|S|ENSG00000188157|AGRN|ENST00000379370|18/36|||1022/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982205	.	G	A	372.27	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.314;DP=1529;Dels=0.00;FS=1.129;HRun=1;HaplotypeScore=1.1177;InbreedingCoeff=-0.0134;MQ=58.00;MQ0=0;MQRankSum=0.488;QD=14.32;ReadPosRankSum=-0.923;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1086K|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gag/Aag|E/K|ENSG00000188157|AGRN|ENST00000379370|19/36|benign(0.32)|tolerated(0.41)|1086/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982403	.	C	T	1164.33	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-2.215;DP=1442;Dels=0.00;FS=2.421;HRun=1;HaplotypeScore=0.9843;InbreedingCoeff=-0.0334;MQ=57.51;MQ0=0;MQRankSum=0.119;QD=10.49;ReadPosRankSum=-1.415;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982444	.	A	G	24810.69	.	AC=102;AF=0.8500;AN=120;BaseQRankSum=4.056;DP=908;Dels=0.00;FS=0.946;HRun=3;HaplotypeScore=0.5521;InbreedingCoeff=0.0418;MQ=57.33;MQ0=0;MQRankSum=0.383;QD=27.94;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982462	.	T	C	27335.24	.	AC=119;AF=0.9917;AN=120;BaseQRankSum=0.923;DP=796;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5400;InbreedingCoeff=-0.0264;MQ=57.04;MQ0=0;MQRankSum=0.157;QD=34.34;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982482	.	C	T	1093.25	.	AC=3;AF=0.0254;AN=118;BaseQRankSum=0.161;DP=714;Dels=0.00;FS=1.368;HRun=0;HaplotypeScore=0.5694;InbreedingCoeff=-0.0414;MQ=57.13;MQ0=0;MQRankSum=0.077;QD=14.20;ReadPosRankSum=3.205;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982484	.	C	T	1096.42	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.607;DP=707;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5118;InbreedingCoeff=-0.0484;MQ=57.24;MQ0=0;MQRankSum=0.555;QD=14.43;ReadPosRankSum=3.144;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982513	.	T	C	22111.8	.	AC=107;AF=0.8917;AN=120;BaseQRankSum=1.897;DP=701;Dels=0.00;FS=6.392;HRun=0;HaplotypeScore=0.5397;InbreedingCoeff=0.3020;MQ=57.59;MQ0=0;MQRankSum=-0.108;QD=32.37;ReadPosRankSum=0.738;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982573	.	C	T	1076.33	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=0.536;DP=905;Dels=0.00;FS=13.480;HRun=0;HaplotypeScore=0.6754;InbreedingCoeff=-0.0368;MQ=58.37;MQ0=0;MQRankSum=-0.537;QD=12.23;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982844	.	G	C	4135.57	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.942;DP=1958;Dels=0.00;FS=2.777;HRun=0;HaplotypeScore=1.2617;InbreedingCoeff=-0.1015;MQ=58.19;MQ0=0;MQRankSum=1.346;QD=12.09;ReadPosRankSum=2.109;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982865	.	A	G	36.62	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.110;DP=1923;Dels=0.00;FS=2.301;HRun=0;HaplotypeScore=1.0780;InbreedingCoeff=-0.0085;MQ=58.17;MQ0=0;MQRankSum=-1.323;QD=5.23;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982906	.	G	A	170.75	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.574;DP=1942;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9590;InbreedingCoeff=-0.0085;MQ=58.80;MQ0=0;MQRankSum=0.287;QD=11.38;ReadPosRankSum=-1.149;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982941	.	T	C	66725.31	.	AC=101;AF=0.8417;AN=120;BaseQRankSum=6.926;DP=2345;Dels=0.00;FS=18.520;HRun=3;HaplotypeScore=1.4495;InbreedingCoeff=0.1870;MQ=58.87;MQ0=0;MQRankSum=0.922;QD=29.91;ReadPosRankSum=-2.729;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	982994	.	T	C	93842.13	.	AC=104;AF=0.8667;AN=120;BaseQRankSum=1.394;DP=3268;Dels=0.00;FS=0.376;HRun=1;HaplotypeScore=1.8496;InbreedingCoeff=0.1346;MQ=58.74;MQ0=0;MQRankSum=1.734;QD=30.11;ReadPosRankSum=-2.989;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|2),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1186|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|2/3||||retained_intron|1,synonymous_variant|ttT/ttC|F|ENSG00000188157|AGRN|ENST00000379370|21/36|||1186/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	983005	.	G	A	980.3	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.923;DP=3454;Dels=0.00;FS=1.269;HRun=0;HaplotypeScore=1.9623;InbreedingCoeff=-0.0084;MQ=58.65;MQ0=0;MQRankSum=1.298;QD=13.62;ReadPosRankSum=2.603;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|2),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R1190H|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|2/3||||retained_intron|1,missense_variant|cGc/cAc|R/H|ENSG00000188157|AGRN|ENST00000379370|21/36|benign(0.252)|tolerated(0.19)|1190/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	983291	.	C	G	40.75	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-3.182;DP=508;Dels=0.00;FS=19.277;HRun=1;HaplotypeScore=0.5577;InbreedingCoeff=-0.0586;MQ=54.43;MQ0=0;MQRankSum=-1.088;QD=0.85;ReadPosRankSum=-2.005;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|22),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984147	.	CAAAAAAAAAAA	C	4515.7	.	AC=46;AF=0.460;AN=100;BaseQRankSum=7.017;DP=179;FS=0.000;HRun=22;HaplotypeScore=47.7401;InbreedingCoeff=0.1656;MQ=37.04;MQ0=0;MQRankSum=-0.993;QD=36.71;ReadPosRankSum=4.302;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984170	.	GCA	G	2088.76	.	AC=73;AF=0.6404;AN=114;BaseQRankSum=8.221;DP=284;FS=0.000;HRun=0;HaplotypeScore=52.8663;InbreedingCoeff=0.0057;MQ=43.30;MQ0=0;MQRankSum=-4.981;QD=8.29;ReadPosRankSum=6.043;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984171	.	CAG	C	6456.64	.	AC=72;AF=0.6207;AN=116;BaseQRankSum=5.599;DP=294;FS=0.921;HRun=0;HaplotypeScore=45.6091;InbreedingCoeff=-0.0184;MQ=43.76;MQ0=0;MQRankSum=-4.138;QD=26.03;ReadPosRankSum=5.090;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984202	.	A	G	219.31	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=-2.549;DP=472;Dels=0.00;FS=8.756;HRun=0;HaplotypeScore=1.0667;InbreedingCoeff=-0.0548;MQ=49.93;MQ0=0;MQRankSum=1.399;QD=7.83;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984257	.	C	T	182.2	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.337;DP=770;Dels=0.00;FS=9.908;HRun=0;HaplotypeScore=0.4996;InbreedingCoeff=-0.0252;MQ=54.84;MQ0=0;MQRankSum=1.233;QD=12.15;ReadPosRankSum=-0.369;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1372|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000188157|AGRN|ENST00000379370|24/36|||1372/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984272	.	C	T	98.86	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=-0.517;DP=781;Dels=0.00;FS=1.477;HRun=2;HaplotypeScore=0.5249;InbreedingCoeff=-0.0341;MQ=54.72;MQ0=0;MQRankSum=0.805;QD=3.95;ReadPosRankSum=0.353;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1377|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|24/36|||1377/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984302	.	T	C	14311.5	.	AC=73;AF=0.6186;AN=118;BaseQRankSum=1.074;DP=888;Dels=0.00;FS=38.864;HRun=1;HaplotypeScore=0.6522;InbreedingCoeff=-0.0933;MQ=54.70;MQ0=0;MQRankSum=1.221;QD=18.54;ReadPosRankSum=0.025;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1387|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|acT/acC|T|ENSG00000188157|AGRN|ENST00000379370|24/36|||1387/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1
chr1	984456	.	C	T	37.75	.	AC=2;AF=0.0175;AN=114;BaseQRankSum=0.621;DP=348;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=0.7641;InbreedingCoeff=-0.0607;MQ=53.36;MQ0=0;MQRankSum=0.580;QD=2.90;ReadPosRankSum=-0.096;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984476	.	T	G	35.43	.	AC=6;AF=0.060;AN=100;BaseQRankSum=-3.204;DP=227;Dels=0.01;FS=3.373;HRun=3;HaplotypeScore=0.9086;InbreedingCoeff=-0.1488;MQ=48.96;MQ0=0;MQRankSum=-3.544;QD=1.07;ReadPosRankSum=1.813;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984480	.	C	G	43.98	.	AC=7;AF=0.071;AN=98;BaseQRankSum=-3.119;DP=215;Dels=0.00;FS=2.297;HRun=4;HaplotypeScore=2.0881;InbreedingCoeff=-0.1728;MQ=47.60;MQ0=0;MQRankSum=-4.127;QD=1.47;ReadPosRankSum=3.119;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984485	.	A	G	61.07	.	AC=8;AF=0.083;AN=96;BaseQRankSum=-3.712;DP=196;Dels=0.02;FS=2.293;HRun=4;HaplotypeScore=2.7170;InbreedingCoeff=-0.0981;MQ=45.76;MQ0=0;MQRankSum=-5.008;QD=2.35;ReadPosRankSum=3.158;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984489	.	G	T	64.93	.	AC=2;AF=0.021;AN=96;BaseQRankSum=1.248;DP=184;Dels=0.00;FS=2.430;HRun=0;HaplotypeScore=2.0202;InbreedingCoeff=0.0358;MQ=44.34;MQ0=0;MQRankSum=0.975;QD=21.64;ReadPosRankSum=-0.342;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984489	.	GAC	G	147.88	.	AC=19;AF=0.1863;AN=102;BaseQRankSum=5.670;DP=170;FS=16.798;HRun=0;HaplotypeScore=44.7087;InbreedingCoeff=-0.0321;MQ=43.36;MQ0=0;MQRankSum=-5.590;QD=2.39;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984494	.	GC	G	1466.1	.	AC=57;AF=0.663;AN=86;BaseQRankSum=2.571;DP=152;FS=2.990;HRun=1;HaplotypeScore=47.8858;InbreedingCoeff=0.1367;MQ=40.49;MQ0=0;MQRankSum=-2.751;QD=11.64;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984501	.	A	G	452.7	.	AC=26;AF=0.317;AN=82;BaseQRankSum=0.750;DP=155;Dels=0.04;FS=57.535;HRun=7;HaplotypeScore=2.7737;InbreedingCoeff=-0.1078;MQ=40.74;MQ0=0;MQRankSum=-5.758;QD=5.73;ReadPosRankSum=3.176;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984510	.	C	CG	61.68	.	AC=13;AF=0.144;AN=90;BaseQRankSum=4.890;DP=164;FS=70.003;HRun=4;HaplotypeScore=50.6057;InbreedingCoeff=-0.0152;MQ=42.03;MQ0=0;MQRankSum=-4.938;QD=1.50;ReadPosRankSum=-1.662;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984524	.	T	G	47.35	.	AC=11;AF=0.125;AN=88;BaseQRankSum=-2.019;DP=191;Dels=0.01;FS=48.423;HRun=3;HaplotypeScore=3.1841;InbreedingCoeff=-0.0001;MQ=47.05;MQ0=0;MQRankSum=-3.798;QD=1.01;ReadPosRankSum=3.652;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984528	.	T	G	133.69	.	AC=15;AF=0.167;AN=90;BaseQRankSum=-2.316;DP=208;Dels=0.01;FS=63.386;HRun=4;HaplotypeScore=2.2156;InbreedingCoeff=-0.0134;MQ=47.68;MQ0=0;MQRankSum=-5.136;QD=2.09;ReadPosRankSum=3.074;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984533	.	T	G	92.45	.	AC=10;AF=0.111;AN=90;BaseQRankSum=-2.508;DP=221;Dels=0.00;FS=75.206;HRun=4;HaplotypeScore=0.9453;InbreedingCoeff=0.0314;MQ=49.13;MQ0=0;MQRankSum=-5.147;QD=1.71;ReadPosRankSum=0.969;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984711	.	G	A	778.12	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.444;DP=2749;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.7477;InbreedingCoeff=-0.0101;MQ=58.27;MQ0=0;MQRankSum=-0.471;QD=11.61;ReadPosRankSum=-0.316;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1465Q|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cGg/cAg|R/Q|ENSG00000188157|AGRN|ENST00000379370|25/36|benign(0.094)|tolerated(0.53)|1465/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|2/2||||retained_intron|1
chr1	984847	.	G	C	1888.19	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.596;DP=3896;Dels=0.00;FS=5.841;HRun=0;HaplotypeScore=3.8645;InbreedingCoeff=-0.0190;MQ=58.46;MQ0=0;MQRankSum=0.505;QD=13.58;ReadPosRankSum=-1.173;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|25),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984888	.	A	G	1593.23	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.251;DP=2785;Dels=0.00;FS=2.468;HRun=0;HaplotypeScore=2.4818;InbreedingCoeff=-0.0179;MQ=58.39;MQ0=0;MQRankSum=2.076;QD=14.75;ReadPosRankSum=3.534;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|25),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	984957	.	G	A	998.45	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.493;DP=2152;Dels=0.00;FS=5.524;HRun=0;HaplotypeScore=1.2695;InbreedingCoeff=-0.0190;MQ=58.57;MQ0=0;MQRankSum=-0.059;QD=17.83;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1509Q|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cGg/cAg|R/Q|ENSG00000188157|AGRN|ENST00000379370|26/36|possibly_damaging(0.459)|tolerated(0.3)|1509/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985165	.	C	T	53.15	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.519;DP=760;Dels=0.00;FS=6.936;HRun=0;HaplotypeScore=0.5648;InbreedingCoeff=-0.0414;MQ=58.09;MQ0=0;MQRankSum=0.442;QD=3.32;ReadPosRankSum=1.429;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1578|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000188157|AGRN|ENST00000379370|26/36|||1578/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985239	.	C	T	170.83	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.190;DP=977;Dels=0.00;FS=9.028;HRun=0;HaplotypeScore=0.4363;InbreedingCoeff=-0.0324;MQ=58.40;MQ0=0;MQRankSum=-0.599;QD=6.57;ReadPosRankSum=0.946;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|26),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985266	.	C	T	19790.42	.	AC=69;AF=0.5750;AN=120;BaseQRankSum=-0.605;DP=1126;Dels=0.00;FS=27.225;HRun=0;HaplotypeScore=0.6765;InbreedingCoeff=-0.0986;MQ=58.34;MQ0=0;MQRankSum=-0.994;QD=19.93;ReadPosRankSum=-1.430;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|26),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985378	.	G	A	349.18	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.347;DP=1151;Dels=0.00;FS=36.082;HRun=1;HaplotypeScore=0.7396;InbreedingCoeff=-0.0111;MQ=57.13;MQ0=0;MQRankSum=0.215;QD=14.55;ReadPosRankSum=1.577;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1614K|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gag/Aag|E/K|ENSG00000188157|AGRN|ENST00000379370|27/36|benign(0.087)|tolerated(0.36)|1614/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985443	.	AG	A	5524.19	.	AC=63;AF=0.5250;AN=120;BaseQRankSum=-4.267;DP=1211;FS=1.118;HRun=15;HaplotypeScore=183.6608;InbreedingCoeff=0.2307;MQ=52.69;MQ0=0;MQRankSum=2.703;QD=6.02;ReadPosRankSum=0.541;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985445	.	G	GT	4225.58	.	AC=52;AF=0.4333;AN=120;BaseQRankSum=0.352;DP=1238;FS=80.878;HRun=0;HaplotypeScore=191.8295;InbreedingCoeff=-0.1480;MQ=52.62;MQ0=0;MQRankSum=2.617;QD=4.70;ReadPosRankSum=-5.379;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985446	.	G	T	10415.52	.	AC=55;AF=0.4583;AN=120;BaseQRankSum=-15.323;DP=1238;Dels=0.00;FS=78.688;HRun=0;HaplotypeScore=12.5413;InbreedingCoeff=-0.0418;MQ=52.62;MQ0=0;MQRankSum=3.979;QD=11.59;ReadPosRankSum=-1.572;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985447	.	G	T	432.38	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-5.349;DP=1263;Dels=0.00;FS=3.447;HRun=0;HaplotypeScore=12.2057;InbreedingCoeff=-0.0488;MQ=52.38;MQ0=0;MQRankSum=-2.193;QD=3.90;ReadPosRankSum=0.844;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985449	.	G	A	14507.18	.	AC=74;AF=0.6167;AN=120;BaseQRankSum=-12.718;DP=1283;Dels=0.00;FS=44.752;HRun=0;HaplotypeScore=13.5390;InbreedingCoeff=-0.3559;MQ=52.41;MQ0=0;MQRankSum=2.768;QD=12.78;ReadPosRankSum=-2.687;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985450	.	G	A	9694.98	.	AC=38;AF=0.3167;AN=120;BaseQRankSum=-9.217;DP=1307;Dels=0.00;FS=25.729;HRun=0;HaplotypeScore=14.9791;InbreedingCoeff=-0.3897;MQ=52.45;MQ0=0;MQRankSum=4.412;QD=10.72;ReadPosRankSum=2.909;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985458	.	GT	G	311.7	.	AC=16;AF=0.1333;AN=120;BaseQRankSum=4.206;DP=1448;FS=204.972;HRun=2;HaplotypeScore=201.5164;InbreedingCoeff=-0.1309;MQ=53.65;MQ0=0;MQRankSum=1.914;QD=0.64;ReadPosRankSum=10.293;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985460	.	T	C	3061.71	.	AC=16;AF=0.1333;AN=120;BaseQRankSum=-0.490;DP=1456;Dels=0.00;FS=6.540;HRun=0;HaplotypeScore=4.9126;InbreedingCoeff=0.2588;MQ=53.76;MQ0=0;MQRankSum=-0.066;QD=11.78;ReadPosRankSum=0.826;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985509	.	G	A	2780.67	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.579;DP=2940;Dels=0.00;FS=10.079;HRun=0;HaplotypeScore=1.7811;InbreedingCoeff=-0.0096;MQ=56.77;MQ0=0;MQRankSum=2.214;QD=17.60;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985662	.	C	T	105.9	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-11.359;DP=3310;Dels=0.00;FS=122.177;HRun=2;HaplotypeScore=2.7454;InbreedingCoeff=-0.0439;MQ=57.76;MQ0=0;MQRankSum=-6.298;QD=0.47;ReadPosRankSum=-5.444;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1643|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|28/36|||1643/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985797	.	A	G	944.49	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.428;DP=2302;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3924;InbreedingCoeff=-0.0171;MQ=57.79;MQ0=0;MQRankSum=2.462;QD=13.12;ReadPosRankSum=0.537;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|28),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985826	.	G	A	438.23	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.507;DP=2255;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1410;InbreedingCoeff=-0.0085;MQ=57.85;MQ0=0;MQRankSum=0.635;QD=14.61;ReadPosRankSum=-0.381;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1666I|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gtc/Atc|V/I|ENSG00000188157|AGRN|ENST00000379370|29/36|benign(0.119)|tolerated(0.44)|1666/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985855	.	C	T	288.16	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.233;DP=2094;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0217;InbreedingCoeff=-0.0087;MQ=58.10;MQ0=0;MQRankSum=0.034;QD=11.53;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1675|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000188157|AGRN|ENST00000379370|29/36|||1675/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985900	.	C	T	558.67	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.271;DP=2177;Dels=0.00;FS=1.593;HRun=2;HaplotypeScore=1.0978;InbreedingCoeff=-0.0209;MQ=58.11;MQ0=0;MQRankSum=0.567;QD=10.16;ReadPosRankSum=-1.144;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1690|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|29/36|||1690/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	985999	.	G	T	316.5	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.550;DP=1428;Dels=0.00;FS=4.252;HRun=0;HaplotypeScore=0.7980;InbreedingCoeff=-0.0179;MQ=58.27;MQ0=0;MQRankSum=0.065;QD=8.79;ReadPosRankSum=0.661;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|29),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986038	.	G	A	80.39	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.606;DP=1099;Dels=0.00;FS=1.750;HRun=0;HaplotypeScore=0.5655;InbreedingCoeff=-0.0135;MQ=57.65;MQ0=0;MQRankSum=0.062;QD=8.04;ReadPosRankSum=0.009;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|29),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986285	.	C	T	224.77	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=0.797;DP=1956;Dels=0.00;FS=30.697;HRun=0;HaplotypeScore=1.3276;InbreedingCoeff=-0.0312;MQ=54.91;MQ0=0;MQRankSum=2.696;QD=12.49;ReadPosRankSum=-0.681;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986286	.	C	T	649.39	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.566;DP=1981;Dels=0.00;FS=22.049;HRun=0;HaplotypeScore=1.6726;InbreedingCoeff=-0.0217;MQ=54.94;MQ0=0;MQRankSum=4.757;QD=11.39;ReadPosRankSum=1.099;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986443	.	C	T	41215.18	.	AC=100;AF=0.8621;AN=116;BaseQRankSum=0.781;DP=1363;Dels=0.00;FS=2.212;HRun=0;HaplotypeScore=0.8018;InbreedingCoeff=0.1240;MQ=57.18;MQ0=0;MQRankSum=-1.053;QD=31.27;ReadPosRankSum=-1.007;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986737	.	T	C	414.03	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.032;DP=1137;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7186;InbreedingCoeff=-0.0327;MQ=58.21;MQ0=0;MQRankSum=1.287;QD=8.63;ReadPosRankSum=2.285;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1786|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggT/ggC|G|ENSG00000188157|AGRN|ENST00000379370|31/36|||1786/2045|protein_coding|1,synonymous_variant|ggT/ggC|G|ENSG00000188157|AGRN|ENST00000419249|4/9|||89/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986885	.	T	G	155.26	.	AC=7;AF=0.0593;AN=118;BaseQRankSum=-10.562;DP=745;Dels=0.00;FS=53.331;HRun=2;HaplotypeScore=0.5798;InbreedingCoeff=-0.0971;MQ=57.41;MQ0=0;MQRankSum=1.830;QD=1.14;ReadPosRankSum=-2.492;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V1808G|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|gTg/gGg|V/G|ENSG00000188157|AGRN|ENST00000379370|32/36|possibly_damaging(0.727)|tolerated(0.14)|1808/2045|protein_coding|1,missense_variant|gTg/gGg|V/G|ENSG00000188157|AGRN|ENST00000419249|5/9|possibly_damaging(0.723)|tolerated(0.1)|111/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	986920	.	C	A	169.9	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.934;DP=839;Dels=0.00;FS=1.422;HRun=0;HaplotypeScore=0.7669;InbreedingCoeff=-0.0288;MQ=58.26;MQ0=0;MQRankSum=0.709;QD=10.62;ReadPosRankSum=2.238;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R1820|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|Cgg/Agg|R|ENSG00000188157|AGRN|ENST00000379370|32/36|||1820/2045|protein_coding|1,synonymous_variant|Cgg/Agg|R|ENSG00000188157|AGRN|ENST00000419249|5/9|||123/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987200	.	C	T	92501.43	.	AC=100;AF=0.8333;AN=120;BaseQRankSum=1.193;DP=3392;Dels=0.00;FS=27.772;HRun=0;HaplotypeScore=2.0645;InbreedingCoeff=0.1600;MQ=56.45;MQ0=0;MQRankSum=1.254;QD=28.89;ReadPosRankSum=-2.661;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987253	.	C	T	635.19	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.926;DP=2121;Dels=0.00;FS=5.063;HRun=0;HaplotypeScore=1.9053;InbreedingCoeff=-0.0356;MQ=53.70;MQ0=0;MQRankSum=0.039;QD=7.22;ReadPosRankSum=-2.083;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987311	.	T	C	44.81	.	AC=8;AF=0.0667;AN=120;BaseQRankSum=-7.260;DP=1543;Dels=0.00;FS=87.443;HRun=3;HaplotypeScore=1.4824;InbreedingCoeff=0.0204;MQ=46.77;MQ0=0;MQRankSum=0.941;QD=0.41;ReadPosRankSum=-2.570;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987341	.	C	T	217.82	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.265;DP=1310;Dels=0.00;FS=10.232;HRun=0;HaplotypeScore=1.1876;InbreedingCoeff=-0.0145;MQ=48.15;MQ0=0;MQRankSum=2.296;QD=7.03;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987342	.	G	A	259.15	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-4.057;DP=1247;Dels=0.00;FS=1.217;HRun=0;HaplotypeScore=1.1837;InbreedingCoeff=-0.0234;MQ=48.33;MQ0=0;MQRankSum=1.716;QD=5.76;ReadPosRankSum=0.808;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987436	.	A	G	63.69	.	AC=9;AF=0.0865;AN=104;BaseQRankSum=2.297;DP=458;Dels=0.00;FS=20.190;HRun=0;HaplotypeScore=0.9717;InbreedingCoeff=-0.0835;MQ=56.48;MQ0=0;MQRankSum=-5.343;QD=0.49;ReadPosRankSum=-3.854;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	987670	.	T	G	1282.33	.	AC=44;AF=0.846;AN=52;BaseQRankSum=-0.078;DP=47;Dels=0.00;FS=6.479;HRun=0;HaplotypeScore=0.0222;InbreedingCoeff=0.1213;MQ=59.01;MQ0=0;MQRankSum=-1.300;QD=30.53;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	988932	.	G	C	36554.37	.	AC=79;AF=0.7596;AN=104;BaseQRankSum=-0.433;DP=1556;Dels=0.00;FS=2.118;HRun=3;HaplotypeScore=0.6684;InbreedingCoeff=0.1833;MQ=57.12;MQ0=0;MQRankSum=-1.108;QD=26.28;ReadPosRankSum=-0.844;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	989423	.	G	A	1179.93	.	AC=6;AF=0.0500;AN=120;BaseQRankSum=-0.586;DP=696;Dels=0.00;FS=1.039;HRun=0;HaplotypeScore=0.3917;InbreedingCoeff=0.5564;MQ=58.43;MQ0=0;MQRankSum=0.139;QD=23.14;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	989461	.	G	A	47.93	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.647;DP=465;Dels=0.00;FS=5.710;HRun=0;HaplotypeScore=0.2114;InbreedingCoeff=-0.0294;MQ=58.14;MQ0=0;MQRankSum=-0.206;QD=5.99;ReadPosRankSum=1.402;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	989500	.	G	A	537.75	.	AC=8;AF=0.0678;AN=118;BaseQRankSum=0.771;DP=317;Dels=0.00;FS=1.526;HRun=1;HaplotypeScore=0.4247;InbreedingCoeff=0.2291;MQ=57.86;MQ0=0;MQRankSum=1.486;QD=19.21;ReadPosRankSum=-0.692;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1
chr1	989811	.	C	A	1223.0	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.075;DP=1715;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1951;InbreedingCoeff=-0.0226;MQ=58.98;MQ0=0;MQRankSum=0.887;QD=11.87;ReadPosRankSum=-0.484;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1
chr1	989847	.	C	T	704.05	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.110;DP=2200;Dels=0.00;FS=6.860;HRun=1;HaplotypeScore=1.7382;InbreedingCoeff=-0.0131;MQ=58.83;MQ0=0;MQRankSum=-0.133;QD=10.67;ReadPosRankSum=0.559;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1966|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,synonymous_variant|Ctg/Ttg|L|ENSG00000188157|AGRN|ENST00000379370|35/36|||1966/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|2/3||||retained_intron|1
chr1	990213	.	C	T	965.08	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.966;DP=1603;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3432;InbreedingCoeff=-0.0258;MQ=58.45;MQ0=0;MQRankSum=0.239;QD=15.57;ReadPosRankSum=-0.735;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1997L|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,missense_variant|cCg/cTg|P/L|ENSG00000188157|AGRN|ENST00000379370|36/36|possibly_damaging(0.612)|deleterious(0.04)|1997/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990280	.	C	T	40484.94	.	AC=89;AF=0.7672;AN=116;BaseQRankSum=-1.914;DP=1861;Dels=0.00;FS=0.408;HRun=0;HaplotypeScore=1.6608;InbreedingCoeff=-0.0422;MQ=58.21;MQ0=0;MQRankSum=1.964;QD=23.35;ReadPosRankSum=-2.688;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D2019|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,synonymous_variant|gaC/gaT|D|ENSG00000188157|AGRN|ENST00000379370|36/36|||2019/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990380	.	C	T	8429.21	.	AC=25;AF=0.2119;AN=118;BaseQRankSum=-1.731;DP=1638;Dels=0.00;FS=19.219;HRun=0;HaplotypeScore=0.9542;InbreedingCoeff=0.0822;MQ=58.01;MQ0=0;MQRankSum=-0.121;QD=14.79;ReadPosRankSum=1.180;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990417	.	T	C	8344.97	.	AC=27;AF=0.2328;AN=116;BaseQRankSum=-1.168;DP=1150;Dels=0.00;FS=1.555;HRun=0;HaplotypeScore=0.4386;InbreedingCoeff=0.0986;MQ=57.95;MQ0=0;MQRankSum=-0.663;QD=16.33;ReadPosRankSum=-1.059;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990517	.	C	T	9650.24	.	AC=75;AF=0.798;AN=94;BaseQRankSum=1.624;DP=348;Dels=0.00;FS=0.641;HRun=0;HaplotypeScore=0.4773;InbreedingCoeff=0.1734;MQ=57.98;MQ0=0;MQRankSum=0.522;QD=30.54;ReadPosRankSum=1.100;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990557	.	C	T	59.21	.	AC=1;AF=0.011;AN=90;BaseQRankSum=2.271;DP=279;Dels=0.00;FS=2.553;HRun=0;HaplotypeScore=0.3165;InbreedingCoeff=-0.0942;MQ=57.30;MQ0=0;MQRankSum=0.765;QD=8.46;ReadPosRankSum=-0.239;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990773	.	C	T	25625.67	.	AC=51;AF=0.689;AN=74;BaseQRankSum=-0.671;DP=1023;Dels=0.00;FS=8.374;HRun=0;HaplotypeScore=0.7685;InbreedingCoeff=0.2919;MQ=57.82;MQ0=0;MQRankSum=0.992;QD=27.26;ReadPosRankSum=1.535;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990806	.	G	A	25266.48	.	AC=55;AF=0.764;AN=72;BaseQRankSum=-2.112;DP=1071;Dels=0.00;FS=2.830;HRun=0;HaplotypeScore=0.8208;InbreedingCoeff=0.2300;MQ=58.13;MQ0=0;MQRankSum=-0.461;QD=25.63;ReadPosRankSum=0.166;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990839	.	C	T	1668.45	.	AC=2;AF=0.029;AN=70;BaseQRankSum=1.196;DP=1096;Dels=0.00;FS=1.633;HRun=2;HaplotypeScore=0.6892;InbreedingCoeff=-0.0818;MQ=58.31;MQ0=0;MQRankSum=1.390;QD=12.27;ReadPosRankSum=-2.018;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990943	.	G	C	216.41	.	AC=1;AF=0.019;AN=52;BaseQRankSum=-0.081;DP=536;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6541;InbreedingCoeff=-0.0441;MQ=58.64;MQ0=0;MQRankSum=-0.296;QD=10.31;ReadPosRankSum=-0.366;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	990984	.	G	A	3835.45	.	AC=33;AF=0.786;AN=42;BaseQRankSum=-0.791;DP=131;Dels=0.00;FS=7.195;HRun=0;HaplotypeScore=0.1328;InbreedingCoeff=0.2454;MQ=58.69;MQ0=0;MQRankSum=-2.076;QD=32.78;ReadPosRankSum=-1.157;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1
chr1	1102069	.	A	G	744.18	.	AC=36;AF=0.900;AN=40;BaseQRankSum=-0.783;DP=29;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0800;InbreedingCoeff=0.1040;MQ=56.74;MQ0=0;MQRankSum=0.679;QD=32.36;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102296	.	G	A	783.47	.	AC=4;AF=0.0357;AN=112;BaseQRankSum=-0.578;DP=498;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2286;InbreedingCoeff=0.2474;MQ=55.59;MQ0=0;MQRankSum=0.771;QD=18.22;ReadPosRankSum=0.212;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102360	.	T	G	216.82	.	AC=16;AF=0.1379;AN=116;BaseQRankSum=-10.289;DP=1092;Dels=0.00;FS=25.292;HRun=4;HaplotypeScore=1.6139;InbreedingCoeff=-0.2074;MQ=53.49;MQ0=0;MQRankSum=2.414;QD=0.71;ReadPosRankSum=7.754;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102563	.	G	A	1052.38	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.152;DP=4513;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.2999;InbreedingCoeff=-0.0179;MQ=56.60;MQ0=0;MQRankSum=2.502;QD=14.03;ReadPosRankSum=-0.938;EFF=EXON(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|1),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000207730|MIR200B|ENST00000384997|1/1||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102657	.	C	T	464.41	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=0.429;DP=1409;Dels=0.00;FS=2.023;HRun=0;HaplotypeScore=1.5640;InbreedingCoeff=-0.0230;MQ=53.83;MQ0=0;MQRankSum=0.937;QD=12.90;ReadPosRankSum=0.639;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102674	.	G	A	964.97	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=0.337;DP=1131;Dels=0.00;FS=1.614;HRun=0;HaplotypeScore=1.4083;InbreedingCoeff=-0.0229;MQ=55.34;MQ0=0;MQRankSum=1.906;QD=12.21;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1102717	.	C	T	175.26	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.432;DP=649;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.6822;InbreedingCoeff=-0.0345;MQ=56.83;MQ0=0;MQRankSum=1.021;QD=9.22;ReadPosRankSum=1.763;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103049	.	C	T	201.32	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.756;DP=465;Dels=0.00;FS=3.302;HRun=0;HaplotypeScore=0.3840;InbreedingCoeff=-0.0481;MQ=57.23;MQ0=0;MQRankSum=0.101;QD=9.15;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103150	.	G	A	13784.17	.	AC=26;AF=0.2281;AN=114;BaseQRankSum=2.288;DP=1923;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8331;InbreedingCoeff=0.0633;MQ=56.95;MQ0=0;MQRankSum=6.711;QD=19.50;ReadPosRankSum=1.282;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103231	.	C	G	920.65	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.613;DP=4071;Dels=0.00;FS=1.295;HRun=0;HaplotypeScore=2.5754;InbreedingCoeff=-0.0143;MQ=57.14;MQ0=0;MQRankSum=0.020;QD=9.59;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103423	.	GA	G	310.03	.	AC=11;AF=0.0932;AN=118;BaseQRankSum=3.186;DP=1367;FS=7.032;HRun=1;HaplotypeScore=112.5777;InbreedingCoeff=-0.1319;MQ=56.78;MQ0=0;MQRankSum=-1.054;QD=1.13;ReadPosRankSum=-12.462;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103424	.	A	G	291.86	.	AC=11;AF=0.0932;AN=118;BaseQRankSum=-4.363;DP=1367;Dels=0.01;FS=12.595;HRun=3;HaplotypeScore=1.1874;InbreedingCoeff=-0.1339;MQ=56.78;MQ0=0;MQRankSum=-0.884;QD=0.96;ReadPosRankSum=-10.797;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103436	.	C	T	253.89	.	AC=1;AF=0.0094;AN=106;BaseQRankSum=1.346;DP=1176;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0420;InbreedingCoeff=-0.0281;MQ=56.38;MQ0=0;MQRankSum=-1.314;QD=7.25;ReadPosRankSum=-3.184;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103471	.	C	T	3129.31	.	AC=41;AF=0.3596;AN=114;BaseQRankSum=7.298;DP=802;Dels=0.00;FS=25.877;HRun=0;HaplotypeScore=0.4705;InbreedingCoeff=-0.6199;MQ=56.31;MQ0=0;MQRankSum=4.884;QD=4.53;ReadPosRankSum=-15.448;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103479	.	G	C	231.39	.	AC=9;AF=0.0804;AN=112;BaseQRankSum=-1.555;DP=715;Dels=0.00;FS=4.645;HRun=2;HaplotypeScore=0.4522;InbreedingCoeff=-0.1256;MQ=56.12;MQ0=0;MQRankSum=1.010;QD=2.22;ReadPosRankSum=-8.435;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103537	.	C	T	42.98	.	AC=4;AF=0.0364;AN=110;BaseQRankSum=-0.058;DP=526;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3527;InbreedingCoeff=0.3068;MQ=56.99;MQ0=0;MQRankSum=1.015;QD=14.33;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103542	.	T	C	13387.36	.	AC=101;AF=0.9182;AN=110;BaseQRankSum=2.524;DP=466;Dels=0.00;FS=6.051;HRun=2;HaplotypeScore=0.2267;InbreedingCoeff=0.0050;MQ=57.11;MQ0=0;MQRankSum=1.977;QD=29.29;ReadPosRankSum=-2.662;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103690	.	T	TCA	4213.79	.	AC=60;AF=0.909;AN=66;BaseQRankSum=-2.219;DP=87;FS=4.960;HRun=0;HaplotypeScore=8.2650;InbreedingCoeff=0.2982;MQ=60.22;MQ0=0;MQRankSum=-0.386;QD=52.02;ReadPosRankSum=-1.623;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1103958	.	T	G	972.47	.	AC=38;AF=0.905;AN=42;BaseQRankSum=0.039;DP=33;Dels=0.00;FS=2.722;HRun=0;HaplotypeScore=0.0376;InbreedingCoeff=0.1168;MQ=59.30;MQ0=0;MQRankSum=0.973;QD=31.37;ReadPosRankSum=-0.195;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1
chr1	1104406	.	C	CCAGA	1690.42	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.911;DP=3757;FS=4.900;HRun=0;HaplotypeScore=321.6033;InbreedingCoeff=-0.0086;MQ=57.98;MQ0=0;MQRankSum=-8.640;QD=27.71;ReadPosRankSum=0.563;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),EXON(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|1),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000198976|MIR429|ENST00000362106|1/1||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1
chr1	1104418	.	A	C	1306.94	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.348;DP=3836;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.7746;InbreedingCoeff=-0.0084;MQ=57.98;MQ0=0;MQRankSum=-0.429;QD=15.38;ReadPosRankSum=1.041;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),EXON(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|1),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000198976|MIR429|ENST00000362106|1/1||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1
chr1	1104584	.	T	C	2225.46	.	AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.668;DP=1142;Dels=0.00;FS=2.698;HRun=0;HaplotypeScore=0.5785;InbreedingCoeff=0.5329;MQ=58.24;MQ0=0;MQRankSum=1.566;QD=23.93;ReadPosRankSum=1.120;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,downstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1
chr1	1104624	.	C	T	353.09	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.668;DP=653;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6949;InbreedingCoeff=-0.0240;MQ=57.96;MQ0=0;MQRankSum=0.018;QD=15.35;ReadPosRankSum=0.448;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,downstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1
chr1	1115086	.	C	T	1455.37	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=-2.311;DP=1823;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0613;InbreedingCoeff=-0.0319;MQ=58.20;MQ0=0;MQRankSum=0.635;QD=14.13;ReadPosRankSum=-1.886;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G56|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G56|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379289|5/16|||56/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379290|5/16|||56/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115187	.	C	T	128.35	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.636;DP=678;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5936;InbreedingCoeff=-0.0317;MQ=57.89;MQ0=0;MQRankSum=0.815;QD=14.26;ReadPosRankSum=0.228;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),START_GAINED(LOW||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115210	.	G	A	3468.51	.	AC=23;AF=0.1983;AN=116;BaseQRankSum=-0.114;DP=539;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6710;InbreedingCoeff=0.0851;MQ=58.05;MQ0=0;MQRankSum=-0.518;QD=16.84;ReadPosRankSum=-1.559;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115213	.	G	T	2687.22	.	AC=21;AF=0.1810;AN=116;BaseQRankSum=0.184;DP=530;Dels=0.00;FS=4.737;HRun=1;HaplotypeScore=0.7398;InbreedingCoeff=0.1254;MQ=58.19;MQ0=0;MQRankSum=0.107;QD=15.10;ReadPosRankSum=-1.774;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),START_GAINED(LOW||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115222	.	C	T	45.39	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.693;DP=471;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3240;InbreedingCoeff=-0.0359;MQ=58.17;MQ0=0;MQRankSum=0.038;QD=5.67;ReadPosRankSum=-1.442;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115379	.	G	A	616.46	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=0.553;DP=584;Dels=0.00;FS=2.233;HRun=0;HaplotypeScore=0.3425;InbreedingCoeff=-0.0782;MQ=58.20;MQ0=0;MQRankSum=1.750;QD=9.94;ReadPosRankSum=0.385;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1
chr1	1115415	.	C	T	177.42	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.248;DP=752;Dels=0.00;FS=3.560;HRun=0;HaplotypeScore=0.6217;InbreedingCoeff=-0.0287;MQ=58.39;MQ0=0;MQRankSum=1.308;QD=8.06;ReadPosRankSum=-0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G67|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G67|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,splice_region_variant&synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379289|6/16|||67/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379290|6/16|||67/673|protein_coding|1,splice_region_variant&5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|2/9|||-/404|protein_coding|1
chr1	1115461	.	C	T	331.7	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.166;DP=949;Dels=0.00;FS=1.152;HRun=0;HaplotypeScore=0.9760;InbreedingCoeff=-0.0264;MQ=58.65;MQ0=0;MQRankSum=1.177;QD=12.76;ReadPosRankSum=1.958;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R10W|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R83W|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R83W|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.28)|tolerated(0.08)|83/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.28)|tolerated(0.08)|83/673|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.365)|deleterious(0.03)|10/404|protein_coding|1
chr1	1115503	.	T	C	1171.08	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=1.533;DP=1103;Dels=0.00;FS=7.100;HRun=1;HaplotypeScore=0.5750;InbreedingCoeff=-0.0426;MQ=59.00;MQ0=0;MQRankSum=1.371;QD=12.59;ReadPosRankSum=-1.312;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C24R|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C97R|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C97R|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.004)|tolerated(0.53)|97/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.004)|tolerated(0.53)|97/673|protein_coding|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.016)|tolerated(0.27)|24/404|protein_coding|1
chr1	1115601	.	C	T	368.82	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.437;DP=1078;Dels=0.00;FS=12.205;HRun=0;HaplotypeScore=0.6665;InbreedingCoeff=-0.0165;MQ=58.97;MQ0=0;MQRankSum=0.473;QD=12.29;ReadPosRankSum=2.503;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N129|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N129|673|TTLL10|protein_coding|CODING|ENST00000379290|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N56|404|TTLL10|protein_coding|CODING|ENST00000379288|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379289|6/16|||129/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379290|6/16|||129/673|protein_coding|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379288|2/9|||56/404|protein_coding|1
chr1	1115605	.	G	T	78.84	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.557;DP=1031;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6145;InbreedingCoeff=-0.0171;MQ=58.95;MQ0=0;MQRankSum=0.835;QD=4.93;ReadPosRankSum=0.136;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A131S|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A131S|673|TTLL10|protein_coding|CODING|ENST00000379290|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A58S|404|TTLL10|protein_coding|CODING|ENST00000379288|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.021)|tolerated(0.07)|131/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.021)|tolerated(0.07)|131/673|protein_coding|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.087)|tolerated(0.07)|58/404|protein_coding|1
chr1	1115739	.	C	T	563.52	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.563;DP=900;Dels=0.00;FS=2.949;HRun=0;HaplotypeScore=0.6729;InbreedingCoeff=-0.0307;MQ=58.26;MQ0=0;MQRankSum=1.624;QD=17.61;ReadPosRankSum=1.518;EFF=INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|6),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1115840	.	AC	A	723.63	.	AC=2;AF=0.0175;AN=114;BaseQRankSum=1.500;DP=1665;FS=3.486;HRun=5;HaplotypeScore=137.9849;InbreedingCoeff=-0.0404;MQ=57.81;MQ0=0;MQRankSum=1.153;QD=10.19;ReadPosRankSum=1.601;EFF=INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|6),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1115994	.	G	A	10204.82	.	AC=24;AF=0.2000;AN=120;BaseQRankSum=-0.160;DP=1696;Dels=0.00;FS=0.223;HRun=0;HaplotypeScore=1.0682;InbreedingCoeff=0.0308;MQ=58.03;MQ0=0;MQRankSum=0.094;QD=16.57;ReadPosRankSum=1.260;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|3),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|7),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1116005	.	C	T	537.05	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.435;DP=1666;Dels=0.00;FS=14.791;HRun=0;HaplotypeScore=1.1478;InbreedingCoeff=-0.0145;MQ=58.06;MQ0=0;MQRankSum=1.799;QD=13.43;ReadPosRankSum=-0.495;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|3),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|7),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1116231	.	T	C	4814.31	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=2.445;DP=1389;Dels=0.00;FS=6.355;HRun=2;HaplotypeScore=1.7202;InbreedingCoeff=0.1639;MQ=56.15;MQ0=0;MQRankSum=1.206;QD=15.28;ReadPosRankSum=0.519;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V176A|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V249A|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V249A|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379289|8/16|benign(0)|tolerated(1)|249/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|2/2||||retained_intron|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379290|8/16|benign(0)|tolerated(1)|249/673|protein_coding|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379288|4/9|benign(0)|tolerated(1)|176/404|protein_coding|1
chr1	1116311	.	A	G	3493.8	.	AC=48;AF=0.4706;AN=102;BaseQRankSum=7.547;DP=286;Dels=0.01;FS=2.211;HRun=0;HaplotypeScore=0.9639;InbreedingCoeff=0.0983;MQ=52.73;MQ0=0;MQRankSum=0.694;QD=18.89;ReadPosRankSum=0.096;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|4),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|8),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117111	.	T	C	797.3	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.679;DP=2103;Dels=0.00;FS=1.613;HRun=4;HaplotypeScore=1.6462;InbreedingCoeff=-0.0099;MQ=57.76;MQ0=0;MQRankSum=1.258;QD=16.61;ReadPosRankSum=-0.652;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|4),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|8),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117200	.	A	ACTCAG	2202.05	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-4.680;DP=3092;FS=21.350;HRun=0;HaplotypeScore=287.1827;InbreedingCoeff=-0.0395;MQ=57.35;MQ0=0;MQRankSum=-7.883;QD=28.60;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117398	.	A	G	8833.57	.	AC=60;AF=0.5172;AN=116;BaseQRankSum=3.163;DP=557;Dels=0.00;FS=2.617;HRun=0;HaplotypeScore=0.4621;InbreedingCoeff=0.0835;MQ=57.86;MQ0=0;MQRankSum=1.868;QD=22.25;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117486	.	A	G	1272.34	.	AC=17;AF=0.1441;AN=118;BaseQRankSum=-1.118;DP=292;Dels=0.00;FS=2.091;HRun=0;HaplotypeScore=0.1964;InbreedingCoeff=-0.1365;MQ=57.43;MQ0=0;MQRankSum=0.534;QD=14.14;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117529	.	A	C	317.04	.	AC=5;AF=0.0424;AN=118;BaseQRankSum=-1.360;DP=362;Dels=0.00;FS=1.548;HRun=1;HaplotypeScore=0.4341;InbreedingCoeff=-0.0846;MQ=57.60;MQ0=0;MQRankSum=0.707;QD=9.61;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117709	.	G	A	2986.58	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=1.592;DP=3059;Dels=0.00;FS=8.817;HRun=1;HaplotypeScore=1.5659;InbreedingCoeff=-0.0345;MQ=59.00;MQ0=0;MQRankSum=-1.150;QD=12.82;ReadPosRankSum=-4.568;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1117795	.	C	G	1423.49	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.182;DP=4738;Dels=0.00;FS=1.073;HRun=1;HaplotypeScore=2.2289;InbreedingCoeff=-0.0084;MQ=59.08;MQ0=0;MQRankSum=-0.250;QD=14.53;ReadPosRankSum=2.714;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H222Q|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H295Q|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H295Q|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379289|10/16|benign(0.046)|tolerated(0.21)|295/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|3/5||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379290|10/16|benign(0.046)|tolerated(0.21)|295/673|protein_coding|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379288|6/9|benign(0.085)|tolerated(0.23)|222/404|protein_coding|1
chr1	1118119	.	G	A	94.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.954;DP=605;Dels=0.00;FS=6.112;HRun=0;HaplotypeScore=0.5514;InbreedingCoeff=-0.0360;MQ=57.50;MQ0=0;MQRankSum=0.026;QD=15.75;ReadPosRankSum=-0.231;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118157	.	C	T	629.37	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.602;DP=775;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.4619;InbreedingCoeff=-0.0286;MQ=57.49;MQ0=0;MQRankSum=1.353;QD=15.73;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118212	.	T	C	16130.03	.	AC=48;AF=0.4068;AN=118;BaseQRankSum=1.657;DP=1395;Dels=0.00;FS=12.889;HRun=1;HaplotypeScore=1.7343;InbreedingCoeff=0.1338;MQ=57.23;MQ0=0;MQRankSum=3.897;QD=20.34;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118244	.	C	T	1034.91	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.695;DP=2048;Dels=0.00;FS=2.342;HRun=0;HaplotypeScore=1.2560;InbreedingCoeff=-0.0165;MQ=57.74;MQ0=0;MQRankSum=0.426;QD=10.78;ReadPosRankSum=-0.861;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118275	.	C	T	6047.77	.	AC=9;AF=0.0750;AN=120;BaseQRankSum=-1.144;DP=2721;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3228;InbreedingCoeff=-0.0826;MQ=57.77;MQ0=0;MQRankSum=4.599;QD=12.68;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C239|404|TTLL10|protein_coding|CODING|ENST00000379288|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379289|11/16|||312/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|4/5||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379290|11/16|||312/673|protein_coding|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379288|7/9|||239/404|protein_coding|1
chr1	1118491	.	A	G	315.28	.	AC=4;AF=0.0339;AN=118;BaseQRankSum=-1.758;DP=1080;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.0651;InbreedingCoeff=-0.0464;MQ=56.58;MQ0=0;MQRankSum=0.706;QD=10.87;ReadPosRankSum=0.829;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118522	.	G	A	231.29	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=0.115;DP=734;Dels=0.00;FS=22.046;HRun=0;HaplotypeScore=0.5763;InbreedingCoeff=-0.0479;MQ=55.98;MQ0=0;MQRankSum=0.916;QD=10.51;ReadPosRankSum=-2.177;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118529	.	G	C	35.12	.	AC=5;AF=0.0431;AN=116;BaseQRankSum=-3.621;DP=699;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6631;InbreedingCoeff=0.1223;MQ=55.74;MQ0=0;MQRankSum=-0.031;QD=1.60;ReadPosRankSum=-2.064;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118560	.	C	T	120.5	.	AC=4;AF=0.0339;AN=118;BaseQRankSum=0.441;DP=502;Dels=0.00;FS=2.806;HRun=0;HaplotypeScore=0.5435;InbreedingCoeff=0.0953;MQ=53.92;MQ0=0;MQRankSum=2.564;QD=9.27;ReadPosRankSum=-0.278;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1118578	.	G	A	921.34	.	AC=9;AF=0.0804;AN=112;BaseQRankSum=-0.517;DP=400;Dels=0.00;FS=2.546;HRun=1;HaplotypeScore=0.3066;InbreedingCoeff=-0.0266;MQ=53.56;MQ0=0;MQRankSum=0.375;QD=14.86;ReadPosRankSum=2.525;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119080	.	T	C	90.74	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=0.742;DP=369;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3252;InbreedingCoeff=-0.0596;MQ=58.29;MQ0=0;MQRankSum=0.380;QD=12.96;ReadPosRankSum=-0.100;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119399	.	C	T	1267.07	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.885;DP=8859;DS;Dels=0.00;FS=6.806;HRun=0;HaplotypeScore=4.5609;InbreedingCoeff=-0.0084;MQ=59.04;MQ0=0;MQRankSum=-1.312;QD=11.73;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H323|404|TTLL10|protein_coding|CODING|ENST00000379288|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H396|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H396|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379289|12/16|||396/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379290|12/16|||396/673|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379288|8/9|||323/404|protein_coding|1
chr1	1119543	.	G	C	392.87	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.504;DP=2292;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8936;InbreedingCoeff=-0.0096;MQ=59.06;MQ0=0;MQRankSum=0.601;QD=13.55;ReadPosRankSum=-1.427;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119546	.	G	T	1327.72	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.808;DP=2166;Dels=0.00;FS=1.426;HRun=1;HaplotypeScore=1.8266;InbreedingCoeff=-0.0272;MQ=59.08;MQ0=0;MQRankSum=-0.008;QD=14.59;ReadPosRankSum=-1.147;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119657	.	G	C	5454.82	.	AC=49;AF=0.4375;AN=112;BaseQRankSum=3.181;DP=432;Dels=0.00;FS=3.269;HRun=3;HaplotypeScore=0.4863;InbreedingCoeff=0.1117;MQ=58.71;MQ0=0;MQRankSum=1.349;QD=20.58;ReadPosRankSum=-0.252;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119796	.	C	T	91.64	.	AC=5;AF=0.078;AN=64;BaseQRankSum=-0.197;DP=63;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1159;InbreedingCoeff=-0.0863;MQ=58.22;MQ0=0;MQRankSum=0.250;QD=9.16;ReadPosRankSum=-0.408;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1119858	.	C	T	125.02	.	AC=7;AF=0.130;AN=54;BaseQRankSum=-0.015;DP=50;Dels=0.00;FS=4.112;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.0152;MQ=56.27;MQ0=0;MQRankSum=0.412;QD=13.89;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1120091	.	G	A	172.79	.	AC=11;AF=0.145;AN=76;BaseQRankSum=0.184;DP=127;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1032;InbreedingCoeff=0.0586;MQ=42.08;MQ0=0;MQRankSum=-1.381;QD=4.80;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1120307	.	G	A	5288.32	.	AC=23;AF=0.235;AN=98;BaseQRankSum=-0.512;DP=784;Dels=0.00;FS=3.693;HRun=0;HaplotypeScore=0.5879;InbreedingCoeff=0.2421;MQ=53.35;MQ0=0;MQRankSum=3.646;QD=18.62;ReadPosRankSum=1.917;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1120337	.	G	A	33.77	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.146;DP=1640;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8805;InbreedingCoeff=-0.0159;MQ=54.17;MQ0=0;MQRankSum=2.540;QD=0.70;ReadPosRankSum=2.633;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1120343	.	C	T	699.62	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.743;DP=1871;Dels=0.00;FS=5.662;HRun=0;HaplotypeScore=1.0425;InbreedingCoeff=-0.0085;MQ=54.11;MQ0=0;MQRankSum=0.033;QD=16.66;ReadPosRankSum=2.495;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1
chr1	1120370	.	C	G	708.51	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.070;DP=2729;Dels=0.00;FS=2.564;HRun=0;HaplotypeScore=1.4361;InbreedingCoeff=-0.0084;MQ=54.85;MQ0=0;MQRankSum=2.839;QD=10.12;ReadPosRankSum=1.250;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L355V|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L428V|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L428V|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379289|13/16|probably_damaging(0.951)|tolerated(0.12)|428/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379290|13/16|probably_damaging(0.951)|tolerated(0.12)|428/673|protein_coding|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379288|9/9|probably_damaging(0.999)|tolerated(0.12)|355/404|protein_coding|1
chr1	1120377	.	T	A	4655.8	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=1.090;DP=2884;Dels=0.00;FS=2.193;HRun=1;HaplotypeScore=1.7603;InbreedingCoeff=-0.0435;MQ=55.01;MQ0=0;MQRankSum=6.538;QD=16.22;ReadPosRankSum=-0.513;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M357K|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M430K|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M430K|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379289|13/16|benign(0.181)|tolerated(0.99)|430/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379290|13/16|benign(0.181)|tolerated(0.99)|430/673|protein_coding|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379288|9/9|benign(0.088)|tolerated(0.91)|357/404|protein_coding|1
chr1	1120431	.	G	A	10163.92	.	AC=16;AF=0.1333;AN=120;BaseQRankSum=-1.606;DP=3363;Dels=0.00;FS=20.818;HRun=1;HaplotypeScore=1.5931;InbreedingCoeff=0.1346;MQ=56.00;MQ0=0;MQRankSum=8.100;QD=14.38;ReadPosRankSum=1.101;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S375N|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S448N|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S448N|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=missense_variant&NMD_transcript_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000486379|1/5|unknown(0)||6/45|nonsense_mediated_decay|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379289|13/16|benign(0)|tolerated(1)|448/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379290|13/16|benign(0)|tolerated(1)|448/673|protein_coding|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379288|9/9|benign(0)|tolerated(1)|375/404|protein_coding|1
chr1	1120536	.	G	A	3644.72	.	AC=9;AF=0.0750;AN=120;BaseQRankSum=-1.719;DP=1842;Dels=0.00;FS=0.462;HRun=0;HaplotypeScore=1.6538;InbreedingCoeff=0.1586;MQ=56.93;MQ0=0;MQRankSum=7.086;QD=15.99;ReadPosRankSum=-0.320;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1
chr1	1120587	.	G	A	207.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.370;DP=1099;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7829;InbreedingCoeff=-0.0101;MQ=57.36;MQ0=0;MQRankSum=0.481;QD=11.53;ReadPosRankSum=0.161;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1
chr1	1120621	.	T	C	922.19	.	AC=6;AF=0.0500;AN=120;BaseQRankSum=-0.439;DP=752;Dels=0.00;FS=2.007;HRun=0;HaplotypeScore=0.6123;InbreedingCoeff=-0.0575;MQ=57.87;MQ0=0;MQRankSum=1.573;QD=10.72;ReadPosRankSum=-1.626;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1
chr1	1138735	.	C	G	141.37	.	AC=8;AF=0.118;AN=68;BaseQRankSum=-0.596;DP=90;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3854;InbreedingCoeff=0.1736;MQ=56.04;MQ0=0;MQRankSum=-0.664;QD=11.78;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),DOWNSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),DOWNSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1138913	.	T	C	4314.24	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=2.277;DP=804;Dels=0.00;FS=7.205;HRun=4;HaplotypeScore=0.3748;InbreedingCoeff=0.2363;MQ=56.65;MQ0=0;MQRankSum=1.461;QD=20.64;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5),UTR_3_PRIME(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|4);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||-/255|protein_coding|1
chr1	1138963	.	C	T	602.78	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.829;DP=1466;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.7567;InbreedingCoeff=-0.0248;MQ=57.17;MQ0=0;MQRankSum=0.908;QD=8.74;ReadPosRankSum=0.934;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5),UTR_3_PRIME(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|4);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||-/255|protein_coding|1
chr1	1139202	.	T	C	2450.32	.	AC=16;AF=0.1333;AN=120;BaseQRankSum=2.131;DP=874;Dels=0.00;FS=3.615;HRun=0;HaplotypeScore=0.9934;InbreedingCoeff=0.3376;MQ=57.90;MQ0=0;MQRankSum=0.238;QD=14.94;ReadPosRankSum=0.958;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P179|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,synonymous_variant|ccA/ccG|P|ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||179/255|protein_coding|1
chr1	1139216	.	G	A	192.87	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=1.202;DP=865;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6000;InbreedingCoeff=0.3637;MQ=58.10;MQ0=0;MQRankSum=0.774;QD=11.35;ReadPosRankSum=-0.636;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R175C|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,missense_variant|Cgt/Tgt|R/C|ENSG00000186891|TNFRSF18|ENST00000328596|4/4|benign(0)|tolerated(0.09)|175/255|protein_coding|1
chr1	1139498	.	C	T	443.47	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.002;DP=812;Dels=0.00;FS=10.375;HRun=0;HaplotypeScore=0.5381;InbreedingCoeff=-0.0387;MQ=58.91;MQ0=0;MQRankSum=0.153;QD=7.92;ReadPosRankSum=-1.689;EFF=INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V101M|169|TNFRSF18|protein_coding|CODING|ENST00000486728|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V173M|234|TNFRSF18|protein_coding|CODING|ENST00000379265|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V173M|241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000379265|4/5|benign(0.2)|tolerated(0.25)|173/234|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000379268|4/5|benign(0.2)|tolerated(0.26)|173/241|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000486728|3/4|benign(0.2)|tolerated(0.14)|101/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1139862	.	T	C	4003.11	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=2.163;DP=3444;Dels=0.00;FS=24.530;HRun=0;HaplotypeScore=1.7331;InbreedingCoeff=0.3739;MQ=58.49;MQ0=0;MQRankSum=0.567;QD=18.88;ReadPosRankSum=-5.116;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|234|TNFRSF18|protein_coding|CODING|ENST00000379265|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|241|TNFRSF18|protein_coding|CODING|ENST00000379268|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K33|169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000379265|3/5|||105/234|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000379268|3/5|||105/241|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000486728|2/4|||33/169|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000328596|3/4|||105/255|protein_coding|1
chr1	1140290	.	T	C	112.5	.	AC=7;AF=0.146;AN=48;BaseQRankSum=1.165;DP=43;Dels=0.00;FS=8.424;HRun=1;HaplotypeScore=0.0347;InbreedingCoeff=0.1666;MQ=58.92;MQ0=0;MQRankSum=-0.621;QD=16.07;ReadPosRankSum=1.709;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1140336	.	C	A	41.02	.	AC=7;AF=0.175;AN=40;BaseQRankSum=-2.498;DP=35;Dels=0.00;FS=16.166;HRun=3;HaplotypeScore=0.0909;InbreedingCoeff=0.1580;MQ=57.31;MQ0=0;MQRankSum=-0.221;QD=6.84;ReadPosRankSum=-1.676;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1140435	.	G	T	467.03	.	AC=25;AF=0.463;AN=54;BaseQRankSum=-0.385;DP=39;Dels=0.00;FS=1.380;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.2592;MQ=60.00;MQ0=0;MQRankSum=0.014;QD=24.58;ReadPosRankSum=-1.128;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1140504	.	T	C	76.53	.	AC=7;AF=0.090;AN=78;BaseQRankSum=-0.513;DP=85;Dels=0.00;FS=7.579;HRun=4;HaplotypeScore=0.1294;InbreedingCoeff=0.1345;MQ=58.35;MQ0=0;MQRankSum=0.232;QD=9.57;ReadPosRankSum=0.795;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1140812	.	TC	T	426.77	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=3.763;DP=2438;FS=2.359;HRun=1;HaplotypeScore=140.7554;InbreedingCoeff=-0.0094;MQ=58.75;MQ0=0;MQRankSum=1.559;QD=21.34;ReadPosRankSum=0.995;EFF=FRAME_SHIFT(HIGH||-|-11|169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),FRAME_SHIFT(HIGH||-|-83|234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),FRAME_SHIFT(HIGH||-|-83|241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),FRAME_SHIFT(HIGH||-|-83|255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000379265|2/5|||83/234|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000379268|2/5|||83/241|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000486728|1/4|||11/169|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000328596|2/4|||83/255|protein_coding|1
chr1	1141556	.	G	C	130.07	.	AC=7;AF=0.097;AN=72;BaseQRankSum=0.191;DP=66;Dels=0.00;FS=4.782;HRun=3;HaplotypeScore=0.1198;InbreedingCoeff=-0.0389;MQ=57.15;MQ0=0;MQRankSum=-0.406;QD=11.82;ReadPosRankSum=-0.358;EFF=INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|1),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|1),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|1),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1141723	.	A	G	877.55	.	AC=13;AF=0.1204;AN=108;BaseQRankSum=0.547;DP=397;Dels=0.00;FS=2.262;HRun=3;HaplotypeScore=0.1820;InbreedingCoeff=0.0234;MQ=58.98;MQ0=0;MQRankSum=0.061;QD=11.40;ReadPosRankSum=-1.301;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|1),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|1),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|1),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1142399	.	A	AC	117.53	.	AC=8;AF=0.308;AN=26;BaseQRankSum=-2.601;DP=22;FS=0.000;HRun=4;HaplotypeScore=4.5003;InbreedingCoeff=0.4087;MQ=58.95;MQ0=0;MQRankSum=0.702;QD=23.51;ReadPosRankSum=0.537;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1146478	.	T	C	51.13	.	AC=2;AF=0.050;AN=40;BaseQRankSum=-1.556;DP=39;Dels=0.00;FS=14.569;HRun=2;HaplotypeScore=0.1961;InbreedingCoeff=-0.2329;MQ=56.11;MQ0=0;MQRankSum=-1.373;QD=5.11;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1146785	.	G	C	472.67	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.520;DP=773;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3659;InbreedingCoeff=-0.0419;MQ=55.65;MQ0=0;MQRankSum=2.347;QD=10.28;ReadPosRankSum=0.755;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|7);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,3_prime_UTR_variant|||ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1146853	.	G	A	316.99	.	AC=4;AF=0.0339;AN=118;BaseQRankSum=-0.212;DP=1329;Dels=0.00;FS=8.508;HRun=0;HaplotypeScore=1.8407;InbreedingCoeff=-0.0495;MQ=50.41;MQ0=0;MQRankSum=0.063;QD=4.12;ReadPosRankSum=-1.639;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|7);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,3_prime_UTR_variant|||ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1
chr1	1146965	.	G	A	553.08	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.055;DP=3459;Dels=0.00;FS=2.776;HRun=0;HaplotypeScore=2.1270;InbreedingCoeff=-0.0086;MQ=56.15;MQ0=0;MQRankSum=0.024;QD=9.22;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A268|277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||268/277|protein_coding|1
chr1	1147024	.	G	A	429.09	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.041;DP=2325;Dels=0.00;FS=8.212;HRun=1;HaplotypeScore=2.0094;InbreedingCoeff=-0.0086;MQ=56.92;MQ0=0;MQRankSum=-0.049;QD=10.73;ReadPosRankSum=0.293;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|6),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1
chr1	1147243	.	A	C	738.87	.	AC=6;AF=0.0508;AN=118;BaseQRankSum=-0.595;DP=705;Dels=0.00;FS=3.973;HRun=2;HaplotypeScore=0.6191;InbreedingCoeff=-0.0615;MQ=56.78;MQ0=0;MQRankSum=-0.060;QD=13.94;ReadPosRankSum=-0.426;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|5),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1
chr1	1147297	.	G	A	1091.92	.	AC=6;AF=0.0508;AN=118;BaseQRankSum=-0.085;DP=1113;Dels=0.00;FS=5.569;HRun=0;HaplotypeScore=0.7306;InbreedingCoeff=-0.0597;MQ=55.37;MQ0=0;MQRankSum=0.517;QD=12.55;ReadPosRankSum=1.988;EFF=DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|5),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1
chr1	1147337	.	C	T	274.47	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.893;DP=1689;Dels=0.00;FS=5.279;HRun=0;HaplotypeScore=1.6439;InbreedingCoeff=-0.0134;MQ=55.97;MQ0=0;MQRankSum=3.240;QD=11.93;ReadPosRankSum=0.328;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V207M|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186827|TNFRSF4|ENST00000379236|5/7|benign(0.024)|tolerated(0.21)|207/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|4/5||||retained_intron|1
chr1	1147422	.	C	T	34265.37	.	AC=47;AF=0.3917;AN=120;BaseQRankSum=-3.610;DP=3511;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=2.1684;InbreedingCoeff=0.1904;MQ=57.58;MQ0=0;MQRankSum=0.337;QD=16.76;ReadPosRankSum=-0.698;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|4),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E178|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|4/4||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|gaG/gaA|E|ENSG00000186827|TNFRSF4|ENST00000379236|5/7|||178/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|4/5||||retained_intron|1
chr1	1147655	.	G	A	774.9	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=-2.234;DP=863;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5174;InbreedingCoeff=-0.0388;MQ=57.75;MQ0=0;MQRankSum=2.030;QD=11.07;ReadPosRankSum=-0.644;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1147770	.	G	A	69.21	.	AC=2;AF=0.0196;AN=102;BaseQRankSum=-0.351;DP=166;Dels=0.00;FS=2.592;HRun=0;HaplotypeScore=0.1050;InbreedingCoeff=-0.1133;MQ=58.60;MQ0=0;MQRankSum=0.830;QD=7.69;ReadPosRankSum=-1.788;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1147822	.	C	T	59.82	.	AC=2;AF=0.023;AN=88;BaseQRankSum=-1.601;DP=102;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0561;InbreedingCoeff=0.0325;MQ=56.99;MQ0=0;MQRankSum=1.803;QD=11.96;ReadPosRankSum=-2.039;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1147976	.	A	AC	257.05	.	AC=13;AF=0.1182;AN=110;BaseQRankSum=3.114;DP=421;FS=9.449;HRun=9;HaplotypeScore=46.1189;InbreedingCoeff=0.0619;MQ=53.84;MQ0=0;MQRankSum=-4.864;QD=2.79;ReadPosRankSum=-0.046;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1147983	.	C	T	450.24	.	AC=6;AF=0.0545;AN=110;BaseQRankSum=-1.143;DP=492;Dels=0.01;FS=1.490;HRun=0;HaplotypeScore=2.2660;InbreedingCoeff=-0.0917;MQ=53.74;MQ0=0;MQRankSum=-5.572;QD=5.85;ReadPosRankSum=-5.673;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1147985	.	C	A	474.8	.	AC=7;AF=0.0648;AN=108;BaseQRankSum=1.860;DP=505;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=2.2858;InbreedingCoeff=-0.0990;MQ=53.76;MQ0=0;MQRankSum=-5.601;QD=5.59;ReadPosRankSum=-5.790;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1148100	.	G	A	407.86	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.544;DP=1027;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7645;InbreedingCoeff=-0.0459;MQ=57.31;MQ0=0;MQRankSum=2.510;QD=7.16;ReadPosRankSum=-1.015;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|3),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1148354	.	C	G	126.37	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.471;DP=949;Dels=0.00;FS=7.261;HRun=1;HaplotypeScore=0.7234;InbreedingCoeff=-0.0178;MQ=58.63;MQ0=0;MQRankSum=0.297;QD=7.43;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|3),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1148445	.	G	A	646.52	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-2.708;DP=1141;Dels=0.00;FS=9.672;HRun=0;HaplotypeScore=0.7418;InbreedingCoeff=-0.0474;MQ=58.91;MQ0=0;MQRankSum=1.939;QD=10.60;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C99|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|2/4||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|tgC/tgT|C|ENSG00000186827|TNFRSF4|ENST00000379236|3/7|||99/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|2/5||||retained_intron|1
chr1	1149222	.	C	G	291.64	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=1.786;DP=868;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7514;InbreedingCoeff=-0.0246;MQ=55.49;MQ0=0;MQRankSum=1.770;QD=10.80;ReadPosRankSum=1.215;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1149272	.	T	C	57.68	.	AC=9;AF=0.0750;AN=120;BaseQRankSum=-9.463;DP=854;Dels=0.00;FS=62.532;HRun=5;HaplotypeScore=2.2956;InbreedingCoeff=-0.0979;MQ=53.68;MQ0=0;MQRankSum=-8.286;QD=0.57;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1149316	.	C	G	1809.62	.	AC=6;AF=0.0500;AN=120;BaseQRankSum=-2.427;DP=1206;Dels=0.00;FS=7.512;HRun=0;HaplotypeScore=1.0567;InbreedingCoeff=0.2590;MQ=55.74;MQ0=0;MQRankSum=3.245;QD=14.14;ReadPosRankSum=1.300;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1
chr1	1149480	.	G	A	811.03	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.272;DP=1806;Dels=0.00;FS=0.697;HRun=0;HaplotypeScore=1.2218;InbreedingCoeff=-0.0227;MQ=56.24;MQ0=0;MQRankSum=1.175;QD=12.48;ReadPosRankSum=1.574;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R10C|277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000186827|TNFRSF4|ENST00000379236|1/7|unknown(0)|deleterious(0)|10/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|1/5||||retained_intron|1
chr1	1152631	.	C	A	73.67	.	AC=6;AF=0.333;AN=18;BaseQRankSum=1.036;DP=11;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=57.87;MQ0=0;MQRankSum=0.000;QD=18.42;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1152794	.	A	G	38.74	.	AC=6;AF=0.250;AN=24;BaseQRankSum=0.720;DP=37;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.4589;InbreedingCoeff=0.4010;MQ=52.01;MQ0=0;MQRankSum=-2.348;QD=12.91;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1152798	.	A	C	38.42	.	AC=6;AF=0.250;AN=24;BaseQRankSum=0.147;DP=40;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.4236;InbreedingCoeff=0.4263;MQ=52.65;MQ0=0;MQRankSum=-2.740;QD=12.81;ReadPosRankSum=-1.267;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1152800	.	G	C	38.25	.	AC=6;AF=0.250;AN=24;BaseQRankSum=-0.172;DP=40;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1945;InbreedingCoeff=0.4359;MQ=52.65;MQ0=0;MQRankSum=-2.690;QD=12.75;ReadPosRankSum=-2.003;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1152904	.	G	A	446.25	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.116;DP=2117;Dels=0.00;FS=5.998;HRun=0;HaplotypeScore=1.1651;InbreedingCoeff=-0.0085;MQ=59.10;MQ0=0;MQRankSum=0.448;QD=16.53;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H359|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000078808|SDF4|ENST00000360001|7/7|||359/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1153009	.	G	A	2720.69	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.647;DP=5548;Dels=0.00;FS=10.837;HRun=0;HaplotypeScore=3.0829;InbreedingCoeff=0.9964;MQ=59.14;MQ0=0;MQRankSum=-1.581;QD=29.57;ReadPosRankSum=-0.625;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A324|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000360001|7/7|||324/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1153113	.	G	A	16021.84	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=1.612;DP=4750;Dels=0.00;FS=29.208;HRun=1;HaplotypeScore=3.8427;InbreedingCoeff=0.1934;MQ=58.59;MQ0=0;MQRankSum=-0.299;QD=16.67;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L328|348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|ctC/ctT|L|ENSG00000078808|SDF4|ENST00000263741|7/7|||328/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1153658	.	C	T	180.9	.	AC=3;AF=0.0254;AN=118;BaseQRankSum=-1.007;DP=436;Dels=0.00;FS=8.257;HRun=0;HaplotypeScore=0.1613;InbreedingCoeff=-0.0432;MQ=57.74;MQ0=0;MQRankSum=-0.296;QD=10.05;ReadPosRankSum=0.424;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|6),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1153671	.	C	T	201.6	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.401;DP=557;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3657;InbreedingCoeff=-0.0187;MQ=57.34;MQ0=0;MQRankSum=0.747;QD=20.16;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|6),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1154121	.	G	A	626.94	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.070;DP=2668;Dels=0.00;FS=1.726;HRun=0;HaplotypeScore=1.8437;InbreedingCoeff=-0.0088;MQ=57.56;MQ0=0;MQRankSum=2.723;QD=11.61;ReadPosRankSum=-0.999;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|5),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|5),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|5),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1
chr1	1154374	.	G	A	229.71	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.034;DP=1145;Dels=0.00;FS=3.775;HRun=1;HaplotypeScore=0.6454;InbreedingCoeff=-0.0116;MQ=58.50;MQ0=0;MQRankSum=0.802;QD=7.92;ReadPosRankSum=0.928;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000078808|SDF4|ENST00000403997|4/5|possibly_damaging(0.833)|deleterious(0.02)|132/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|1/3||||retained_intron|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1
chr1	1154539	.	G	A	108.45	.	AC=6;AF=0.068;AN=88;BaseQRankSum=-1.095;DP=122;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0697;InbreedingCoeff=0.0875;MQ=56.71;MQ0=0;MQRankSum=-1.837;QD=10.84;ReadPosRankSum=1.197;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1
chr1	1158070	.	C	T	64.6	.	AC=4;AF=0.154;AN=26;BaseQRankSum=-0.623;DP=14;Dels=0.00;FS=2.688;HRun=0;HaplotypeScore=0.1231;InbreedingCoeff=0.1888;MQ=58.33;MQ0=0;MQRankSum=-1.090;QD=21.53;ReadPosRankSum=-1.713;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158277	.	G	A	258.06	.	AC=7;AF=0.0660;AN=106;BaseQRankSum=1.218;DP=155;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0943;InbreedingCoeff=0.0730;MQ=58.19;MQ0=0;MQRankSum=0.130;QD=14.34;ReadPosRankSum=0.779;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158326	.	G	A	805.01	.	AC=13;AF=0.1102;AN=118;BaseQRankSum=1.271;DP=279;Dels=0.00;FS=5.053;HRun=0;HaplotypeScore=0.2930;InbreedingCoeff=0.1676;MQ=57.56;MQ0=0;MQRankSum=-0.687;QD=17.13;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158357	.	A	G	916.43	.	AC=10;AF=0.0833;AN=120;BaseQRankSum=-1.540;DP=426;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2650;InbreedingCoeff=0.0655;MQ=57.91;MQ0=0;MQRankSum=-0.479;QD=14.10;ReadPosRankSum=1.027;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158427	.	C	CTCAT	100.01	.	AC=7;AF=0.0583;AN=120;BaseQRankSum=4.538;DP=1071;FS=0.000;HRun=0;HaplotypeScore=95.9447;InbreedingCoeff=-0.0617;MQ=58.35;MQ0=0;MQRankSum=-4.421;QD=0.89;ReadPosRankSum=1.472;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158441	.	GCA	G	2419.37	.	AC=7;AF=0.0583;AN=120;BaseQRankSum=8.159;DP=1188;FS=0.719;HRun=0;HaplotypeScore=80.9615;InbreedingCoeff=-0.0625;MQ=58.49;MQ0=0;MQRankSum=0.055;QD=13.82;ReadPosRankSum=-1.278;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158534	.	G	GAC	10837.11	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=10.503;DP=3575;FS=3.271;HRun=0;HaplotypeScore=253.2703;InbreedingCoeff=0.0992;MQ=58.17;MQ0=0;MQRankSum=-7.407;QD=20.14;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158543	.	G	A	443.06	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.994;DP=3849;Dels=0.00;FS=6.053;HRun=0;HaplotypeScore=6.1083;InbreedingCoeff=-0.0084;MQ=58.27;MQ0=0;MQRankSum=0.950;QD=14.77;ReadPosRankSum=-2.545;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158562	.	AAC	A	12359.87	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=19.423;DP=4760;FS=4.102;HRun=0;HaplotypeScore=407.7083;InbreedingCoeff=0.0992;MQ=58.43;MQ0=0;MQRankSum=-2.532;QD=17.12;ReadPosRankSum=-0.503;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158567	.	A	G	234.79	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.278;DP=5021;Dels=0.00;FS=38.170;HRun=0;HaplotypeScore=12.5431;InbreedingCoeff=-0.0170;MQ=58.49;MQ0=0;MQRankSum=-1.361;QD=1.06;ReadPosRankSum=-7.229;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158631	.	A	G	241536.85	.	AC=114;AF=0.9500;AN=120;BaseQRankSum=1.928;DP=8050;DS;Dels=0.00;FS=8.602;HRun=0;HaplotypeScore=3.7991;InbreedingCoeff=-0.0526;MQ=58.98;MQ0=0;MQRankSum=-0.435;QD=30.00;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000403997|3/5|||125/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000465727|4/7|||190/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000263741|4/7|||190/348|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000360001|4/7|||190/362|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000545427|4/5|||190/202|protein_coding|1
chr1	1158667	.	G	A	386.78	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.651;DP=8431;DS;Dels=0.00;FS=0.701;HRun=0;HaplotypeScore=4.5114;InbreedingCoeff=-0.0084;MQ=59.13;MQ0=0;MQRankSum=2.552;QD=11.72;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000403997|3/5|||113/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000465727|4/7|||178/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000263741|4/7|||178/348|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000360001|4/7|||178/362|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000545427|4/5|||178/202|protein_coding|1
chr1	1158948	.	A	G	660.52	.	AC=12;AF=0.1034;AN=116;BaseQRankSum=1.771;DP=442;Dels=0.00;FS=0.846;HRun=1;HaplotypeScore=0.2202;InbreedingCoeff=0.0086;MQ=59.04;MQ0=0;MQRankSum=1.540;QD=9.57;ReadPosRankSum=1.061;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158973	.	A	T	563.68	.	AC=11;AF=0.0932;AN=118;BaseQRankSum=-1.928;DP=394;Dels=0.00;FS=3.023;HRun=0;HaplotypeScore=0.2474;InbreedingCoeff=0.1727;MQ=58.52;MQ0=0;MQRankSum=0.128;QD=11.74;ReadPosRankSum=-0.053;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1158975	.	A	C	547.46	.	AC=10;AF=0.0847;AN=118;BaseQRankSum=0.388;DP=392;Dels=0.00;FS=6.029;HRun=1;HaplotypeScore=0.2379;InbreedingCoeff=0.1826;MQ=58.58;MQ0=0;MQRankSum=-0.688;QD=12.73;ReadPosRankSum=0.857;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159020	.	A	G	979.85	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=0.104;DP=496;Dels=0.00;FS=2.803;HRun=0;HaplotypeScore=0.5310;InbreedingCoeff=0.1557;MQ=58.21;MQ0=0;MQRankSum=1.781;QD=13.80;ReadPosRankSum=-2.245;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159024	.	C	T	1054.21	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=1.335;DP=502;Dels=0.00;FS=1.571;HRun=1;HaplotypeScore=0.4565;InbreedingCoeff=0.1688;MQ=58.19;MQ0=0;MQRankSum=-0.153;QD=14.25;ReadPosRankSum=-1.099;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159062	.	T	C	2118.4	.	AC=9;AF=0.0833;AN=108;BaseQRankSum=4.132;DP=759;Dels=0.00;FS=2.568;HRun=0;HaplotypeScore=0.5732;InbreedingCoeff=0.1030;MQ=58.19;MQ0=0;MQRankSum=0.274;QD=18.11;ReadPosRankSum=0.765;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159107	.	G	A	3662.49	.	AC=10;AF=0.0926;AN=108;BaseQRankSum=1.981;DP=1308;Dels=0.00;FS=17.272;HRun=0;HaplotypeScore=1.1121;InbreedingCoeff=0.0871;MQ=52.60;MQ0=0;MQRankSum=2.390;QD=16.35;ReadPosRankSum=1.115;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159165	.	T	TG	273.77	.	AC=12;AF=0.1132;AN=106;BaseQRankSum=7.494;DP=2291;FS=100.981;HRun=1;HaplotypeScore=440.9019;InbreedingCoeff=-0.1415;MQ=41.07;MQ0=0;MQRankSum=-7.908;QD=0.51;ReadPosRankSum=7.023;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159166	.	G	GC	3218.59	.	AC=42;AF=0.3962;AN=106;BaseQRankSum=8.299;DP=2329;FS=244.281;HRun=3;HaplotypeScore=445.7226;InbreedingCoeff=-0.6799;MQ=40.93;MQ0=0;MQRankSum=-10.648;QD=1.55;ReadPosRankSum=6.277;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159170	.	G	C	5417.07	.	AC=46;AF=0.4182;AN=110;BaseQRankSum=-10.941;DP=2442;Dels=0.01;FS=490.296;HRun=4;HaplotypeScore=12.6085;InbreedingCoeff=-0.7658;MQ=41.38;MQ0=0;MQRankSum=-18.721;QD=2.30;ReadPosRankSum=6.341;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159170	.	G	GC	3955.45	.	AC=43;AF=0.3909;AN=110;BaseQRankSum=10.923;DP=2473;FS=560.241;HRun=4;HaplotypeScore=452.2142;InbreedingCoeff=-0.6871;MQ=41.56;MQ0=0;MQRankSum=-13.253;QD=1.73;ReadPosRankSum=9.759;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159174	.	CG	C	53.97	.	AC=7;AF=0.0614;AN=114;BaseQRankSum=10.925;DP=2603;FS=201.126;HRun=1;HaplotypeScore=455.1303;InbreedingCoeff=-0.0824;MQ=42.56;MQ0=0;MQRankSum=-11.905;QD=0.19;ReadPosRankSum=3.289;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159175	.	G	C	12381.61	.	AC=47;AF=0.4123;AN=114;BaseQRankSum=-13.988;DP=2603;Dels=0.01;FS=959.340;HRun=4;HaplotypeScore=13.4110;InbreedingCoeff=-0.7559;MQ=42.56;MQ0=0;MQRankSum=-22.983;QD=4.80;ReadPosRankSum=11.432;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159175	.	G	GC	1388.08	.	AC=33;AF=0.2895;AN=114;BaseQRankSum=15.983;DP=2657;FS=479.390;HRun=4;HaplotypeScore=447.3152;InbreedingCoeff=-0.4239;MQ=42.88;MQ0=0;MQRankSum=-14.282;QD=0.74;ReadPosRankSum=11.216;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159179	.	A	C	7593.73	.	AC=46;AF=0.3898;AN=118;BaseQRankSum=-14.894;DP=2793;Dels=0.01;FS=168.118;HRun=3;HaplotypeScore=10.8241;InbreedingCoeff=-0.6865;MQ=44.03;MQ0=0;MQRankSum=-23.118;QD=2.84;ReadPosRankSum=9.565;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159179	.	A	AC	430.63	.	AC=15;AF=0.1293;AN=116;BaseQRankSum=17.141;DP=2801;FS=268.128;HRun=3;HaplotypeScore=446.6273;InbreedingCoeff=-0.1719;MQ=43.85;MQ0=0;MQRankSum=-15.854;QD=0.50;ReadPosRankSum=8.601;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159182	.	G	C	2435.95	.	AC=35;AF=0.3017;AN=116;BaseQRankSum=-22.569;DP=2867;Dels=0.01;FS=332.999;HRun=4;HaplotypeScore=9.7305;InbreedingCoeff=-0.4479;MQ=44.51;MQ0=0;MQRankSum=-21.997;QD=1.18;ReadPosRankSum=7.752;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159182	.	G	GC	290.6	.	AC=11;AF=0.0948;AN=116;BaseQRankSum=18.934;DP=2960;FS=357.719;HRun=4;HaplotypeScore=463.0417;InbreedingCoeff=-0.1293;MQ=44.74;MQ0=0;MQRankSum=-17.632;QD=0.45;ReadPosRankSum=5.626;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159186	.	CA	C	59.87	.	AC=4;AF=0.0345;AN=116;BaseQRankSum=16.532;DP=3075;FS=138.229;HRun=1;HaplotypeScore=462.1606;InbreedingCoeff=-0.0421;MQ=45.70;MQ0=0;MQRankSum=-13.262;QD=0.31;ReadPosRankSum=-6.897;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159187	.	A	C	8669.24	.	AC=47;AF=0.4052;AN=116;BaseQRankSum=-11.349;DP=3075;Dels=0.01;FS=50.216;HRun=4;HaplotypeScore=10.3138;InbreedingCoeff=-0.7071;MQ=45.70;MQ0=0;MQRankSum=-25.197;QD=2.88;ReadPosRankSum=-1.026;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159187	.	A	AC	38.33	.	AC=3;AF=0.0259;AN=116;BaseQRankSum=18.228;DP=3113;FS=209.724;HRun=4;HaplotypeScore=455.4440;InbreedingCoeff=-0.0431;MQ=45.73;MQ0=0;MQRankSum=-16.454;QD=0.25;ReadPosRankSum=-6.893;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159191	.	A	C	4227.25	.	AC=45;AF=0.3814;AN=118;BaseQRankSum=-16.791;DP=3098;Dels=0.00;FS=55.651;HRun=4;HaplotypeScore=21.4245;InbreedingCoeff=-0.6257;MQ=46.09;MQ0=0;MQRankSum=-20.550;QD=1.47;ReadPosRankSum=-6.333;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159485	.	C	T	1786.91	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.460;DP=676;Dels=0.00;FS=1.200;HRun=0;HaplotypeScore=0.4563;InbreedingCoeff=0.0725;MQ=57.99;MQ0=0;MQRankSum=0.146;QD=16.39;ReadPosRankSum=0.465;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159517	.	T	C	12932.29	.	AC=115;AF=0.9583;AN=120;BaseQRankSum=1.742;DP=373;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2819;InbreedingCoeff=0.1828;MQ=58.44;MQ0=0;MQRankSum=1.074;QD=35.14;ReadPosRankSum=1.392;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159520	.	C	T	92.03	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.994;DP=360;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2826;InbreedingCoeff=-0.0403;MQ=58.45;MQ0=0;MQRankSum=0.711;QD=13.15;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159540	.	G	A	542.38	.	AC=6;AF=0.0517;AN=116;BaseQRankSum=-0.694;DP=294;Dels=0.00;FS=4.088;HRun=0;HaplotypeScore=0.1520;InbreedingCoeff=0.0954;MQ=58.66;MQ0=0;MQRankSum=1.126;QD=17.50;ReadPosRankSum=0.267;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1159729	.	T	G	41.48	.	AC=5;AF=0.119;AN=42;BaseQRankSum=0.407;DP=35;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.0685;MQ=55.69;MQ0=0;MQRankSum=-0.031;QD=10.37;ReadPosRankSum=0.470;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1
chr1	1163767	.	C	T	814.94	.	AC=5;AF=0.0446;AN=112;BaseQRankSum=-1.291;DP=646;Dels=0.00;FS=1.287;HRun=0;HaplotypeScore=0.6392;InbreedingCoeff=0.1958;MQ=57.92;MQ0=0;MQRankSum=-5.203;QD=14.05;ReadPosRankSum=2.369;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1163773	.	C	T	190.62	.	AC=2;AF=0.0182;AN=110;BaseQRankSum=-0.471;DP=694;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6224;InbreedingCoeff=0.4388;MQ=58.00;MQ0=0;MQRankSum=0.927;QD=23.83;ReadPosRankSum=2.443;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1163804	.	C	T	3932.35	.	AC=16;AF=0.1356;AN=118;BaseQRankSum=-5.937;DP=1136;Dels=0.00;FS=0.471;HRun=0;HaplotypeScore=1.9937;InbreedingCoeff=-0.0388;MQ=57.51;MQ0=0;MQRankSum=2.984;QD=13.15;ReadPosRankSum=-2.512;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1163811	.	G	GGACA	6953.39	.	AC=15;AF=0.1271;AN=118;BaseQRankSum=-5.858;DP=1276;FS=21.541;HRun=0;HaplotypeScore=109.0684;InbreedingCoeff=-0.0171;MQ=57.57;MQ0=0;MQRankSum=-14.498;QD=29.97;ReadPosRankSum=1.598;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1163964	.	G	A	5411.83	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=1.794;DP=3215;Dels=0.00;FS=17.078;HRun=0;HaplotypeScore=1.6463;InbreedingCoeff=0.3739;MQ=58.93;MQ0=0;MQRankSum=1.765;QD=20.19;ReadPosRankSum=-3.159;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000403997|1/5|||5/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000465727|2/7|||70/254|nonsense_mediated_decay|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000360001|2/7|||70/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000545427|2/5|||70/202|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000263741|2/7|||70/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164031	.	A	G	2189.26	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=0.524;DP=3658;DS;Dels=0.00;FS=1.511;HRun=0;HaplotypeScore=1.4260;InbreedingCoeff=0.6581;MQ=58.98;MQ0=0;MQRankSum=-0.494;QD=25.46;ReadPosRankSum=2.486;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|202|SDF4|protein_coding|CODING|ENST00000545427|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|348|SDF4|protein_coding|CODING|ENST00000263741|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,missense_variant&NMD_transcript_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000465727|2/7|benign(0.002)|tolerated(0.47)|48/254|nonsense_mediated_decay|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000360001|2/7|benign(0)|tolerated(1)|48/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000545427|2/5|benign(0.002)|tolerated(1)|48/202|protein_coding|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000263741|2/7|benign(0.002)|tolerated(1)|48/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164072	.	C	T	1571.76	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-2.716;DP=2924;DS;Dels=0.00;FS=4.033;HRun=0;HaplotypeScore=1.7879;InbreedingCoeff=0.6581;MQ=59.08;MQ0=0;MQRankSum=-0.133;QD=23.11;ReadPosRankSum=3.483;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000465727|2/7|||34/254|nonsense_mediated_decay|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000360001|2/7|||34/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000545427|2/5|||34/202|protein_coding|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000263741|2/7|||34/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164090	.	T	C	1638.23	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=0.539;DP=2459;Dels=0.00;FS=3.268;HRun=1;HaplotypeScore=1.1248;InbreedingCoeff=0.6578;MQ=59.09;MQ0=0;MQRankSum=-1.281;QD=25.20;ReadPosRankSum=2.166;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000465727|2/7|||28/254|nonsense_mediated_decay|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000360001|2/7|||28/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000545427|2/5|||28/202|protein_coding|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000263741|2/7|||28/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164179	.	G	A	833.67	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.622;DP=1063;Dels=0.00;FS=8.157;HRun=0;HaplotypeScore=0.7297;InbreedingCoeff=0.6212;MQ=58.97;MQ0=0;MQRankSum=1.079;QD=26.89;ReadPosRankSum=2.348;EFF=EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|),UTR_5_PRIME(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),UTR_5_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),UTR_5_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),UTR_5_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|2/7|||-/254|nonsense_mediated_decay|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|2/7|||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000545427|2/5|||-/202|protein_coding|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|2/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164250	.	C	CCA	210.26	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.248;DP=413;FS=0.000;HRun=0;HaplotypeScore=29.3469;InbreedingCoeff=0.3092;MQ=58.65;MQ0=0;MQRankSum=2.358;QD=26.28;ReadPosRankSum=0.652;EFF=EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|),UTR_5_PRIME(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),UTR_5_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),UTR_5_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),UTR_5_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,5_prime_UTR_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727|2/7|||-/254|nonsense_mediated_decay|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001|2/7|||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427|2/5|||-/202|protein_coding|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741|2/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1164687	.	G	C	63.9	.	AC=4;AF=0.118;AN=34;BaseQRankSum=1.043;DP=28;Dels=0.00;FS=10.726;HRun=0;HaplotypeScore=0.2350;InbreedingCoeff=0.1906;MQ=58.33;MQ0=0;MQRankSum=0.241;QD=21.30;ReadPosRankSum=-1.685;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|1),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|1),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|1),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|1),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1
chr1	1168180	.	G	C	380.06	.	AC=9;AF=0.105;AN=86;BaseQRankSum=0.307;DP=108;Dels=0.00;FS=6.481;HRun=3;HaplotypeScore=0.2416;InbreedingCoeff=0.2106;MQ=56.49;MQ0=0;MQRankSum=1.066;QD=21.11;ReadPosRankSum=-1.425;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E174D|329|B3GALT6|protein_coding|CODING|ENST00000379198|),UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|gaG/gaC|E/D|ENSG00000176022|B3GALT6|ENST00000379198|1/1|benign(0.012)|tolerated(0.54)|174/329|protein_coding|1
chr1	1168567	.	G	A	197.95	.	AC=1;AF=0.0098;AN=102;BaseQRankSum=-1.549;DP=173;Dels=0.00;FS=11.564;HRun=1;HaplotypeScore=0.1898;InbreedingCoeff=-0.1063;MQ=57.97;MQ0=0;MQRankSum=0.710;QD=15.23;ReadPosRankSum=-0.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E303|329|B3GALT6|protein_coding|CODING|ENST00000379198|),UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|gaG/gaA|E|ENSG00000176022|B3GALT6|ENST00000379198|1/1|||303/329|protein_coding|1
chr1	1168843	.	C	T	395.96	.	AC=2;AF=0.031;AN=64;BaseQRankSum=1.429;DP=826;Dels=0.00;FS=1.955;HRun=0;HaplotypeScore=1.3582;InbreedingCoeff=-0.0815;MQ=56.66;MQ0=0;MQRankSum=0.858;QD=9.90;ReadPosRankSum=0.063;EFF=UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),UTR_3_PRIME(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|1);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,3_prime_UTR_variant|||ENSG00000176022|B3GALT6|ENST00000379198|1/1|||-/329|protein_coding|1
chr1	1169094	.	G	C	1587.89	.	AC=1;AF=0.016;AN=62;BaseQRankSum=1.089;DP=2518;Dels=0.00;FS=10.659;HRun=0;HaplotypeScore=2.4242;InbreedingCoeff=-0.0613;MQ=58.81;MQ0=0;MQRankSum=1.439;QD=15.72;ReadPosRankSum=-1.308;EFF=UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),UTR_3_PRIME(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|1);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,3_prime_UTR_variant|||ENSG00000176022|B3GALT6|ENST00000379198|1/1|||-/329|protein_coding|1
chr1	1177474	.	A	G	43.95	.	AC=4;AF=0.105;AN=38;BaseQRankSum=-0.867;DP=27;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0000;InbreedingCoeff=0.1376;MQ=58.27;MQ0=0;MQRankSum=0.685;QD=14.65;ReadPosRankSum=1.780;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1177630	.	A	G	581.54	.	AC=7;AF=0.092;AN=76;BaseQRankSum=-0.178;DP=115;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1257;InbreedingCoeff=0.0962;MQ=57.55;MQ0=0;MQRankSum=0.915;QD=24.23;ReadPosRankSum=0.465;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1177773	.	C	G	1999.45	.	AC=2;AF=0.0179;AN=112;BaseQRankSum=0.305;DP=963;Dels=0.00;FS=3.764;HRun=0;HaplotypeScore=0.6634;InbreedingCoeff=0.3008;MQ=56.96;MQ0=0;MQRankSum=1.294;QD=32.25;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1177893	.	C	T	2555.63	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.263;DP=3336;Dels=0.00;FS=2.685;HRun=0;HaplotypeScore=1.5161;InbreedingCoeff=-0.0315;MQ=56.80;MQ0=0;MQRankSum=1.301;QD=12.84;ReadPosRankSum=-1.150;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1
chr1	1177918	.	CT	C	3669.24	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=7.568;DP=3999;DS;FS=3.238;HRun=1;HaplotypeScore=287.5611;InbreedingCoeff=-0.0451;MQ=56.98;MQ0=0;MQRankSum=0.885;QD=11.87;ReadPosRankSum=-0.015;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1
chr1	1177919	.	T	C	61.88	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.136;DP=3999;DS;Dels=0.03;FS=1.983;HRun=6;HaplotypeScore=4.0470;InbreedingCoeff=-0.0307;MQ=56.98;MQ0=0;MQRankSum=0.755;QD=0.41;ReadPosRankSum=-5.282;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1
chr1	1178047	.	T	C	1725.37	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.230;DP=3874;DS;Dels=0.00;FS=5.482;HRun=1;HaplotypeScore=3.6848;InbreedingCoeff=-0.0204;MQ=57.02;MQ0=0;MQRankSum=-0.683;QD=10.59;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|7),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1178244	.	G	C	483.23	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.151;DP=1605;Dels=0.00;FS=2.186;HRun=1;HaplotypeScore=1.4521;InbreedingCoeff=0.7073;MQ=59.01;MQ0=0;MQRankSum=0.273;QD=32.22;ReadPosRankSum=-0.751;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Gta|L261V|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|2/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|Cta/Gta|L/V|ENSG00000184163|FAM132A|ENST00000330388|7/8|benign(0.001)|tolerated(0.98)|261/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1
chr1	1178245	.	C	T	4066.47	.	AC=15;AF=0.1250;AN=120;BaseQRankSum=-1.548;DP=1603;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3636;InbreedingCoeff=0.1530;MQ=59.01;MQ0=0;MQRankSum=1.224;QD=13.51;ReadPosRankSum=-1.253;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T260|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|2/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,synonymous_variant|acG/acA|T|ENSG00000184163|FAM132A|ENST00000330388|7/8|||260/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1
chr1	1178453	.	G	A	466.91	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.075;DP=1354;Dels=0.00;FS=5.034;HRun=0;HaplotypeScore=0.8964;InbreedingCoeff=0.6716;MQ=57.75;MQ0=0;MQRankSum=1.619;QD=23.35;ReadPosRankSum=0.909;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C240|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,synonymous_variant|tgC/tgT|C|ENSG00000184163|FAM132A|ENST00000330388|6/8|||240/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1
chr1	1178482	.	A	G	2936.1	.	AC=13;AF=0.1121;AN=116;BaseQRankSum=2.434;DP=1386;Dels=0.00;FS=2.627;HRun=0;HaplotypeScore=0.8846;InbreedingCoeff=0.1962;MQ=57.58;MQ0=0;MQRankSum=-0.397;QD=11.84;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C231R|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|Tgt/Cgt|C/R|ENSG00000184163|FAM132A|ENST00000330388|6/8|benign(0)|tolerated(1)|231/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1
chr1	1178571	.	C	G	79.76	.	AC=15;AF=0.1364;AN=110;BaseQRankSum=-6.811;DP=485;Dels=0.00;FS=26.762;HRun=6;HaplotypeScore=2.2448;InbreedingCoeff=-0.0971;MQ=52.03;MQ0=0;MQRankSum=-8.725;QD=0.69;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1178576	.	T	G	181.67	.	AC=17;AF=0.1574;AN=108;BaseQRankSum=-5.916;DP=438;Dels=0.01;FS=1.537;HRun=5;HaplotypeScore=3.1212;InbreedingCoeff=-0.0423;MQ=51.34;MQ0=0;MQRankSum=-4.551;QD=1.36;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1178586	.	T	G	169.37	.	AC=15;AF=0.150;AN=100;BaseQRankSum=-5.907;DP=387;Dels=0.00;FS=26.401;HRun=4;HaplotypeScore=3.0709;InbreedingCoeff=-0.2409;MQ=49.88;MQ0=0;MQRankSum=-7.180;QD=1.44;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1178925	.	G	A	1946.86	.	AC=13;AF=0.1102;AN=118;BaseQRankSum=-1.965;DP=1010;Dels=0.00;FS=8.294;HRun=0;HaplotypeScore=0.9315;InbreedingCoeff=0.1268;MQ=57.94;MQ0=0;MQRankSum=0.962;QD=13.91;ReadPosRankSum=-0.443;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A180V|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|3/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|gCc/gTc|A/V|ENSG00000184163|FAM132A|ENST00000330388|5/8|possibly_damaging(0.558)|tolerated(0.06)|180/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1178935	.	G	A	255.43	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=0.108;DP=915;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6695;InbreedingCoeff=-0.0264;MQ=58.14;MQ0=0;MQRankSum=0.476;QD=14.19;ReadPosRankSum=1.215;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179030	.	G	A	765.15	.	AC=11;AF=0.0982;AN=112;BaseQRankSum=-0.728;DP=324;Dels=0.00;FS=3.299;HRun=0;HaplotypeScore=0.2197;InbreedingCoeff=0.1064;MQ=58.27;MQ0=0;MQRankSum=-0.685;QD=17.39;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179309	.	G	A	1486.6	.	AC=12;AF=0.1017;AN=118;BaseQRankSum=-0.202;DP=527;Dels=0.00;FS=5.698;HRun=0;HaplotypeScore=0.2810;InbreedingCoeff=0.1431;MQ=57.09;MQ0=0;MQRankSum=0.038;QD=15.65;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179416	.	A	C	387.28	.	AC=8;AF=0.0690;AN=116;BaseQRankSum=-8.770;DP=848;Dels=0.00;FS=181.958;HRun=3;HaplotypeScore=0.9454;InbreedingCoeff=-0.0952;MQ=53.74;MQ0=0;MQRankSum=-2.436;QD=3.25;ReadPosRankSum=-1.967;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V150G|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|2/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|2/2||||retained_intron|1,missense_variant|gTg/gGg|V/G|ENSG00000184163|FAM132A|ENST00000330388|4/8|possibly_damaging(0.839)|deleterious(0)|150/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179532	.	C	T	490.97	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.132;DP=1835;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0586;InbreedingCoeff=-0.0210;MQ=57.90;MQ0=0;MQRankSum=1.423;QD=10.45;ReadPosRankSum=0.071;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|2),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|3),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|2/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|2/2||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179747	.	C	T	48.72	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.106;DP=2070;Dels=0.00;FS=5.993;HRun=0;HaplotypeScore=1.5289;InbreedingCoeff=-0.0284;MQ=59.19;MQ0=0;MQRankSum=-1.469;QD=6.96;ReadPosRankSum=1.335;EFF=INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|2),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|1),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179800	.	G	A	782.26	.	AC=2;AF=0.0172;AN=116;BaseQRankSum=-3.138;DP=2073;Dels=0.00;FS=2.190;HRun=0;HaplotypeScore=1.3315;InbreedingCoeff=-0.0420;MQ=59.44;MQ0=0;MQRankSum=-0.175;QD=9.78;ReadPosRankSum=0.512;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G85|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|1/2||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000184163|FAM132A|ENST00000330388|2/8|||85/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1179983	.	G	A	2866.16	.	AC=17;AF=0.1417;AN=120;BaseQRankSum=-1.868;DP=688;Dels=0.00;FS=0.855;HRun=0;HaplotypeScore=0.3402;InbreedingCoeff=0.3638;MQ=59.13;MQ0=0;MQRankSum=0.378;QD=21.71;ReadPosRankSum=-2.062;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|1/2||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1181372	.	C	T	142.78	.	AC=9;AF=0.205;AN=44;BaseQRankSum=0.940;DP=56;Dels=0.00;FS=10.677;HRun=0;HaplotypeScore=0.1214;InbreedingCoeff=0.3107;MQ=57.48;MQ0=0;MQRankSum=0.070;QD=20.40;ReadPosRankSum=1.361;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1181751	.	T	C	107.96	.	AC=6;AF=0.130;AN=46;BaseQRankSum=0.029;DP=35;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0398;InbreedingCoeff=0.0106;MQ=56.62;MQ0=0;MQRankSum=0.202;QD=15.42;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1
chr1	1190061	.	A	G	343.05	.	AC=12;AF=0.176;AN=68;BaseQRankSum=1.182;DP=113;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0935;InbreedingCoeff=0.3239;MQ=57.93;MQ0=0;MQRankSum=0.135;QD=20.18;ReadPosRankSum=-0.224;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190166	.	G	A	197.18	.	AC=1;AF=0.017;AN=58;BaseQRankSum=1.290;DP=332;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.5654;InbreedingCoeff=-0.0510;MQ=56.96;MQ0=0;MQRankSum=0.784;QD=10.38;ReadPosRankSum=-0.832;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190206	.	G	A	197.94	.	AC=1;AF=0.015;AN=68;BaseQRankSum=-0.934;DP=520;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7388;InbreedingCoeff=-0.0641;MQ=57.17;MQ0=0;MQRankSum=2.013;QD=15.23;ReadPosRankSum=-0.458;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190207	.	C	T	432.13	.	AC=7;AF=0.100;AN=70;BaseQRankSum=-1.418;DP=529;Dels=0.00;FS=4.930;HRun=0;HaplotypeScore=0.6967;InbreedingCoeff=0.1975;MQ=57.18;MQ0=0;MQRankSum=0.339;QD=9.39;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190481	.	G	A	116.73	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.156;DP=714;Dels=0.00;FS=12.015;HRun=1;HaplotypeScore=0.6509;InbreedingCoeff=-0.0173;MQ=59.06;MQ0=0;MQRankSum=-0.238;QD=6.49;ReadPosRankSum=1.991;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190523	.	C	T	321.56	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.643;DP=1091;Dels=0.00;FS=3.027;HRun=0;HaplotypeScore=0.7506;InbreedingCoeff=-0.0300;MQ=58.89;MQ0=0;MQRankSum=-0.522;QD=7.31;ReadPosRankSum=-0.760;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190544	.	G	A	120.24	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.624;DP=1337;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7866;InbreedingCoeff=-0.0117;MQ=58.85;MQ0=0;MQRankSum=-0.513;QD=4.01;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000360466|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190685	.	G	A	695.66	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.799;DP=3117;Dels=0.00;FS=3.835;HRun=0;HaplotypeScore=1.7262;InbreedingCoeff=-0.0084;MQ=59.01;MQ0=0;MQRankSum=1.046;QD=13.38;ReadPosRankSum=-1.664;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|2),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000347370|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000348298|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000400929|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H191|224|UBE2J2|protein_coding|CODING|ENST00000339385|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H226|259|UBE2J2|protein_coding|CODING|ENST00000349431|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H226|259|UBE2J2|protein_coding|CODING|ENST00000360466|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H242|275|UBE2J2|protein_coding|CODING|ENST00000400930|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|7);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000339385|6/6|||191/224|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|7/7|||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000349431|7/7|||226/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|2/2||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000348298|7/7|||174/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000347370|7/7|||174/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000400930|8/8|||242/275|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000400929|6/6|||174/207|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000360466|7/7|||226/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1190913	.	CT	C	3484.23	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=10.114;DP=1539;FS=1.866;HRun=3;HaplotypeScore=78.4459;InbreedingCoeff=0.1110;MQ=58.86;MQ0=0;MQRankSum=0.337;QD=15.98;ReadPosRankSum=0.968;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|5),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|6),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|6),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|4),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1191290	.	C	T	273.07	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.037;DP=1868;Dels=0.00;FS=4.676;HRun=1;HaplotypeScore=1.1539;InbreedingCoeff=-0.0090;MQ=58.69;MQ0=0;MQRankSum=0.087;QD=11.38;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|5),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|6),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|6),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|4),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1191589	.	G	A	716.56	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.146;DP=2848;Dels=0.00;FS=11.254;HRun=0;HaplotypeScore=1.5890;InbreedingCoeff=-0.0084;MQ=59.49;MQ0=0;MQRankSum=0.568;QD=9.55;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|1/2||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1191651	.	A	G	329.19	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.637;DP=1304;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5306;InbreedingCoeff=-0.0104;MQ=59.58;MQ0=0;MQRankSum=0.314;QD=16.46;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|1/2||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192105	.	C	A	38.15	.	AC=5;AF=0.081;AN=62;BaseQRankSum=0.672;DP=78;Dels=0.00;FS=4.123;HRun=11;HaplotypeScore=0.3295;InbreedingCoeff=-0.0659;MQ=39.13;MQ0=0;MQRankSum=-1.521;QD=4.77;ReadPosRankSum=-0.389;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192268	.	G	A	34.31	.	AC=9;AF=0.0763;AN=118;BaseQRankSum=-2.951;DP=712;Dels=0.00;FS=86.476;HRun=23;HaplotypeScore=4.3915;InbreedingCoeff=-0.1175;MQ=40.22;MQ0=0;MQRankSum=-4.056;QD=0.35;ReadPosRankSum=-6.599;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192321	.	C	A	197.5	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.375;DP=1985;Dels=0.00;FS=2.097;HRun=0;HaplotypeScore=2.7167;InbreedingCoeff=-0.0116;MQ=52.62;MQ0=0;MQRankSum=0.704;QD=10.97;ReadPosRankSum=-0.366;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192515	.	A	G	9144.94	.	AC=10;AF=0.0833;AN=120;BaseQRankSum=-2.796;DP=4520;Dels=0.00;FS=4.056;HRun=0;HaplotypeScore=2.8736;InbreedingCoeff=0.1273;MQ=57.88;MQ0=0;MQRankSum=7.716;QD=16.19;ReadPosRankSum=-1.141;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|3),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|4),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|2),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|2),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192767	.	C	G	279.19	.	AC=5;AF=0.0424;AN=118;BaseQRankSum=-0.503;DP=1028;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.9757;InbreedingCoeff=-0.0595;MQ=43.48;MQ0=0;MQRankSum=0.689;QD=3.49;ReadPosRankSum=-0.850;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192769	.	CG	C	46.23	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=7.490;DP=929;FS=8.084;HRun=1;HaplotypeScore=182.4593;InbreedingCoeff=-0.1268;MQ=41.55;MQ0=0;MQRankSum=-2.659;QD=0.18;ReadPosRankSum=0.739;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192770	.	GCCA	G	709.55	.	AC=36;AF=0.3051;AN=118;BaseQRankSum=7.682;DP=910;FS=3.236;HRun=0;HaplotypeScore=185.0135;InbreedingCoeff=-0.3195;MQ=40.92;MQ0=0;MQRankSum=-5.310;QD=1.24;ReadPosRankSum=5.795;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192771	.	CCA	C	1171.87	.	AC=44;AF=0.3729;AN=118;BaseQRankSum=10.317;DP=897;FS=2.917;HRun=0;HaplotypeScore=180.9024;InbreedingCoeff=-0.3867;MQ=40.58;MQ0=0;MQRankSum=-6.072;QD=1.66;ReadPosRankSum=5.982;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192772	.	CA	C	1504.33	.	AC=45;AF=0.3879;AN=116;BaseQRankSum=10.581;DP=873;FS=9.989;HRun=1;HaplotypeScore=179.8239;InbreedingCoeff=-0.4727;MQ=39.95;MQ0=0;MQRankSum=-6.732;QD=2.06;ReadPosRankSum=6.533;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192773	.	AC	A	268.82	.	AC=52;AF=0.4815;AN=108;BaseQRankSum=1.061;DP=867;FS=7.111;HRun=15;HaplotypeScore=182.8712;InbreedingCoeff=0.1639;MQ=39.70;MQ0=0;MQRankSum=-1.275;QD=0.46;ReadPosRankSum=4.858;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192776	.	C	G	174.83	.	AC=3;AF=0.0273;AN=110;BaseQRankSum=-0.288;DP=833;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=8.8403;InbreedingCoeff=-0.0771;MQ=38.73;MQ0=0;MQRankSum=2.194;QD=3.64;ReadPosRankSum=-1.689;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192786	.	C	A	471.53	.	AC=12;AF=0.1154;AN=104;BaseQRankSum=-6.703;DP=722;Dels=0.00;FS=2.215;HRun=0;HaplotypeScore=1.5194;InbreedingCoeff=0.1443;MQ=35.94;MQ0=0;MQRankSum=0.095;QD=3.27;ReadPosRankSum=2.115;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192786	.	C	CA	288.17	.	AC=16;AF=0.1455;AN=110;BaseQRankSum=0.649;DP=716;FS=2.212;HRun=0;HaplotypeScore=181.3815;InbreedingCoeff=0.2496;MQ=36.10;MQ0=0;MQRankSum=-1.597;QD=1.84;ReadPosRankSum=-0.511;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192787	.	C	G	453.3	.	AC=12;AF=0.120;AN=100;BaseQRankSum=2.173;DP=716;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4128;InbreedingCoeff=0.1641;MQ=36.10;MQ0=0;MQRankSum=-0.721;QD=4.08;ReadPosRankSum=0.454;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192787	.	C	CG	374.1	.	AC=17;AF=0.1545;AN=110;BaseQRankSum=0.800;DP=712;FS=0.000;HRun=0;HaplotypeScore=181.2272;InbreedingCoeff=0.2381;MQ=36.30;MQ0=0;MQRankSum=-3.098;QD=2.65;ReadPosRankSum=-1.333;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192789	.	T	C	74.78	.	AC=1;AF=0.0098;AN=102;BaseQRankSum=-1.047;DP=679;Dels=0.00;FS=0.000;HRun=15;HaplotypeScore=1.3798;InbreedingCoeff=-0.0743;MQ=36.78;MQ0=0;MQRankSum=-1.425;QD=9.35;ReadPosRankSum=1.189;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1192796	.	G	A	212.87	.	AC=4;AF=0.0364;AN=110;BaseQRankSum=-1.973;DP=615;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.2937;InbreedingCoeff=-0.0566;MQ=38.68;MQ0=0;MQRankSum=-0.959;QD=4.09;ReadPosRankSum=-2.635;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1198510	.	G	A	538.65	.	AC=2;AF=0.0179;AN=112;BaseQRankSum=2.023;DP=404;Dels=0.00;FS=3.013;HRun=0;HaplotypeScore=0.4208;InbreedingCoeff=-0.0639;MQ=57.33;MQ0=0;MQRankSum=1.298;QD=17.96;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1198578	.	C	T	938.59	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.880;DP=1202;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1589;InbreedingCoeff=0.4530;MQ=59.30;MQ0=0;MQRankSum=0.985;QD=21.33;ReadPosRankSum=-2.169;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1198618	.	T	A	9157.74	.	AC=14;AF=0.1167;AN=120;BaseQRankSum=0.445;DP=2253;Dels=0.00;FS=1.666;HRun=1;HaplotypeScore=1.0999;InbreedingCoeff=0.1893;MQ=59.34;MQ0=0;MQRankSum=0.163;QD=16.59;ReadPosRankSum=2.122;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1203116	.	G	A	525.11	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.823;DP=1403;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4562;InbreedingCoeff=-0.0106;MQ=58.08;MQ0=0;MQRankSum=2.079;QD=11.93;ReadPosRankSum=2.071;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|2),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|2),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|2),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|2/7|||-/44|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294|2/6|||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752|2/6|||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1203167	.	C	T	1087.43	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.333;DP=2258;Dels=0.00;FS=8.468;HRun=1;HaplotypeScore=1.5625;InbreedingCoeff=0.8365;MQ=57.71;MQ0=0;MQRankSum=-0.200;QD=28.62;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|2),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|2),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|2),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|2/7|||-/44|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294|2/6|||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752|2/6|||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1203271	.	G	A	523.79	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.124;DP=5255;Dels=0.00;FS=0.700;HRun=0;HaplotypeScore=3.4063;InbreedingCoeff=-0.0084;MQ=58.09;MQ0=0;MQRankSum=0.171;QD=10.48;ReadPosRankSum=-1.486;EFF=EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|100|UBE2J2|protein_coding|CODING|ENST00000422076|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|195|UBE2J2|protein_coding|CODING|ENST00000435198|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|259|UBE2J2|protein_coding|CODING|ENST00000349431|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|259|UBE2J2|protein_coding|CODING|ENST00000360466|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|275|UBE2J2|protein_coding|CODING|ENST00000400930|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|42|UBE2J2|protein_coding|CODING|ENST00000488418|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|70|UBE2J2|protein_coding|CODING|ENST00000502382|),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2);CSQ=synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000502382|3/5|||34/71|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000477894|2/6|||34/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|2/3||||retained_intron|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000473215|2/7|||34/44|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000503294|2/6|||34/44|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000464036|2/8|||34/105|nonsense_mediated_decay|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000488418|2/2|||34/43|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000422076|2/5|||34/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000349431|2/7|||34/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|2/7|||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000450390|2/8|||34/43|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000466752|2/6|||34/44|nonsense_mediated_decay|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000400930|2/8|||34/275|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000360466|2/7|||34/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000435198|2/7|||34/196|protein_coding|1
chr1	1203387	.	G	A	3095.18	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-1.839;DP=3379;Dels=0.00;FS=3.622;HRun=0;HaplotypeScore=1.5906;InbreedingCoeff=0.4826;MQ=57.66;MQ0=0;MQRankSum=0.825;QD=17.10;ReadPosRankSum=1.782;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1203464	.	G	A	885.88	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-4.027;DP=1394;Dels=0.00;FS=13.230;HRun=0;HaplotypeScore=0.4057;InbreedingCoeff=-0.0494;MQ=51.99;MQ0=0;MQRankSum=3.105;QD=10.42;ReadPosRankSum=-0.558;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1203573	.	C	T	46.79	.	AC=2;AF=0.0169;AN=118;BaseQRankSum=-2.029;DP=398;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3328;InbreedingCoeff=-0.0477;MQ=57.94;MQ0=0;MQRankSum=0.064;QD=3.90;ReadPosRankSum=-2.020;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1
chr1	1219382	.	C	G	517.5	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.346;DP=1303;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5737;InbreedingCoeff=-0.0262;MQ=56.33;MQ0=0;MQRankSum=-0.677;QD=16.69;ReadPosRankSum=0.201;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q126E|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q28E|704|SCNN1D|protein_coding|CODING|ENST00000325425|),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),STOP_GAINED(HIGH|NONSENSE|tCa/tGa|S29*|138|SCNN1D|protein_coding|CODING|ENST00000470022|),UTR_5_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),UTR_5_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6);CSQ=5_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|3/15|||-/638|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|3/4||||processed_transcript|1,missense_variant&NMD_transcript_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000379101|5/17|benign(0.028)||126/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,missense_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000325425|2/15|benign(0.007)|deleterious(0)|28/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,stop_gained|tCa/tGa|S/*|ENSG00000162572|SCNN1D|ENST00000470022|3/4|||29/139|protein_coding|1,5_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|2/14|||-/638|protein_coding|1,missense_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000379116|5/18|benign(0.007)|deleterious(0)|126/802|protein_coding|1
chr1	1219477	.	T	G	61.09	.	AC=10;AF=0.0962;AN=104;BaseQRankSum=-2.023;DP=228;Dels=0.02;FS=0.000;HRun=9;HaplotypeScore=1.3848;InbreedingCoeff=0.0086;MQ=48.26;MQ0=0;MQRankSum=-5.204;QD=1.61;ReadPosRankSum=5.116;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219487	.	T	G	252.82	.	AC=16;AF=0.178;AN=90;BaseQRankSum=-6.004;DP=169;Dels=0.04;FS=31.669;HRun=9;HaplotypeScore=0.8999;InbreedingCoeff=-0.0964;MQ=41.70;MQ0=0;MQRankSum=-5.947;QD=4.29;ReadPosRankSum=5.203;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219489	.	A	G	510.67	.	AC=22;AF=0.244;AN=90;BaseQRankSum=-4.579;DP=161;Dels=0.04;FS=3.458;HRun=6;HaplotypeScore=0.5978;InbreedingCoeff=-0.2229;MQ=40.79;MQ0=0;MQRankSum=-5.372;QD=6.01;ReadPosRankSum=7.135;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219495	.	GT	G	259.6	.	AC=33;AF=0.434;AN=76;BaseQRankSum=1.135;DP=118;FS=0.000;HRun=1;HaplotypeScore=47.6513;InbreedingCoeff=0.0098;MQ=32.06;MQ0=0;MQRankSum=-2.879;QD=3.05;ReadPosRankSum=1.806;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219503	.	GTT	G	181.28	.	AC=26;AF=0.481;AN=54;BaseQRankSum=1.078;DP=79;FS=0.000;HRun=2;HaplotypeScore=43.9645;InbreedingCoeff=0.2483;MQ=29.00;MQ0=0;MQRankSum=1.524;QD=4.90;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219508	.	GTGA	G	294.79	.	AC=34;AF=0.586;AN=58;BaseQRankSum=0.768;DP=70;FS=4.559;HRun=0;HaplotypeScore=41.3138;InbreedingCoeff=0.0804;MQ=29.00;MQ0=0;MQRankSum=2.030;QD=5.67;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219522	.	GTC	G	520.05	.	AC=42;AF=0.750;AN=56;BaseQRankSum=-1.486;DP=62;FS=0.000;HRun=0;HaplotypeScore=40.8056;InbreedingCoeff=0.1654;MQ=29.00;MQ0=0;MQRankSum=0.412;QD=10.61;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219534	.	GTT	G	272.36	.	AC=31;AF=0.534;AN=58;BaseQRankSum=0.856;DP=61;FS=0.000;HRun=2;HaplotypeScore=38.8244;InbreedingCoeff=0.3057;MQ=29.00;MQ0=0;MQRankSum=1.124;QD=6.64;ReadPosRankSum=0.386;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219556	.	GTT	G	904.28	.	AC=38;AF=0.826;AN=46;BaseQRankSum=2.314;DP=45;FS=0.000;HRun=2;HaplotypeScore=34.7120;InbreedingCoeff=0.2326;MQ=29.00;MQ0=0;MQRankSum=-0.104;QD=23.80;ReadPosRankSum=0.656;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1219565	.	GTT	G	199.22	.	AC=18;AF=0.450;AN=40;BaseQRankSum=1.357;DP=40;FS=3.680;HRun=2;HaplotypeScore=38.8961;InbreedingCoeff=0.2109;MQ=29.00;MQ0=0;MQRankSum=-0.222;QD=7.38;ReadPosRankSum=-1.209;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1220765	.	C	T	169.99	.	AC=1;AF=0.011;AN=92;BaseQRankSum=0.603;DP=202;Dels=0.00;FS=9.170;HRun=0;HaplotypeScore=0.1511;InbreedingCoeff=-0.0821;MQ=58.15;MQ0=0;MQRankSum=1.246;QD=18.89;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1220822	.	G	A	282.41	.	AC=1;AF=0.0096;AN=104;BaseQRankSum=-0.135;DP=459;Dels=0.00;FS=7.514;HRun=0;HaplotypeScore=0.1948;InbreedingCoeff=-0.0472;MQ=57.39;MQ0=0;MQRankSum=-0.080;QD=14.12;ReadPosRankSum=0.116;EFF=INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1220954	.	G	A	9088.59	.	AC=17;AF=0.1574;AN=108;BaseQRankSum=-2.368;DP=1910;Dels=0.00;FS=13.820;HRun=0;HaplotypeScore=1.1187;InbreedingCoeff=0.4214;MQ=58.61;MQ0=0;MQRankSum=-0.837;QD=20.20;ReadPosRankSum=-1.798;EFF=EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|4),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A24T|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S156|802|SCNN1D|protein_coding|CODING|ENST00000379116|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S58|704|SCNN1D|protein_coding|CODING|ENST00000325425|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|4/4||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,synonymous_variant|tcG/tcA|S|ENSG00000162572|SCNN1D|ENST00000325425|3/15|||58/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,synonymous_variant|tcG/tcA|S|ENSG00000162572|SCNN1D|ENST00000379116|6/18|||156/802|protein_coding|1
chr1	1221001	.	A	G	1982.19	.	AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.350;DP=1904;Dels=0.00;FS=4.488;HRun=1;HaplotypeScore=1.2454;InbreedingCoeff=0.3709;MQ=58.84;MQ0=0;MQRankSum=-1.238;QD=25.09;ReadPosRankSum=0.484;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q172R|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q74R|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A39|669|SCNN1D|protein_coding|CODING|ENST00000379110|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,missense_variant|cAg/cGg|Q/R|ENSG00000162572|SCNN1D|ENST00000325425|3/15|benign(0.108)|deleterious(0.04)|74/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,missense_variant|cAg/cGg|Q/R|ENSG00000162572|SCNN1D|ENST00000379116|6/18|benign(0.108)|deleterious(0.01)|172/802|protein_coding|1
chr1	1221018	.	C	T	150.26	.	AC=1;AF=0.0088;AN=114;BaseQRankSum=1.476;DP=1708;Dels=0.00;FS=1.441;HRun=0;HaplotypeScore=0.9012;InbreedingCoeff=-0.0297;MQ=58.90;MQ0=0;MQRankSum=0.438;QD=6.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H178Y|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H80Y|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A45V|669|SCNN1D|protein_coding|CODING|ENST00000379110|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,missense_variant|Cac/Tac|H/Y|ENSG00000162572|SCNN1D|ENST00000325425|3/15|benign(0.022)|tolerated(0.53)|80/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000162572|SCNN1D|ENST00000379116|6/18|benign(0.022)|tolerated(0.15)|178/802|protein_coding|1
chr1	1221054	.	G	T	326.69	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=-1.105;DP=1276;Dels=0.00;FS=1.144;HRun=1;HaplotypeScore=0.9866;InbreedingCoeff=-0.0243;MQ=58.76;MQ0=0;MQRankSum=-1.148;QD=13.07;ReadPosRankSum=0.107;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221055	.	A	G	407.9	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-2.031;DP=1272;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9531;InbreedingCoeff=-0.0269;MQ=58.74;MQ0=0;MQRankSum=-1.920;QD=14.57;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221138	.	G	A	2422.14	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=1.373;DP=714;Dels=0.00;FS=4.157;HRun=0;HaplotypeScore=0.6978;InbreedingCoeff=0.2209;MQ=58.20;MQ0=0;MQRankSum=0.824;QD=19.38;ReadPosRankSum=-0.027;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221164	.	T	C	91.02	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.693;DP=688;Dels=0.00;FS=9.028;HRun=0;HaplotypeScore=0.7707;InbreedingCoeff=-0.0208;MQ=57.89;MQ0=0;MQRankSum=0.498;QD=11.38;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221276	.	C	T	104.85	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.022;DP=641;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3777;InbreedingCoeff=-0.0348;MQ=57.84;MQ0=0;MQRankSum=1.773;QD=6.55;ReadPosRankSum=0.299;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221302	.	A	G	519.74	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=1.538;DP=606;Dels=0.00;FS=12.594;HRun=0;HaplotypeScore=0.3788;InbreedingCoeff=-0.0395;MQ=57.80;MQ0=0;MQRankSum=0.895;QD=14.85;ReadPosRankSum=-0.140;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221488	.	CAA	C	470.7	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=3.941;DP=1231;FS=0.000;HRun=2;HaplotypeScore=83.4816;InbreedingCoeff=-0.0140;MQ=58.74;MQ0=0;MQRankSum=-0.574;QD=21.40;ReadPosRankSum=1.386;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6),FRAME_SHIFT(HIGH||-|-115|669|SCNN1D|protein_coding|CODING|ENST00000379110|9),FRAME_SHIFT(HIGH||-|-120|138|SCNN1D|protein_coding|CODING|ENST00000470022|4),FRAME_SHIFT(HIGH||-|-150|704|SCNN1D|protein_coding|CODING|ENST00000325425|4),FRAME_SHIFT(HIGH||-|-248|802|SCNN1D|protein_coding|CODING|ENST00000379116|7),FRAME_SHIFT(HIGH||-|-84|638|SCNN1D|protein_coding|CODING|ENST00000338555|4),FRAME_SHIFT(HIGH||-|-84|638|SCNN1D|protein_coding|CODING|ENST00000400928|3);CSQ=frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555|4/15|||84/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,frameshift_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101|6/17|||216-217/328|nonsense_mediated_decay|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425|4/15|||150/704|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022|4/4|||120/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928|3/14|||84/638|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116|7/18|||248/802|protein_coding|1
chr1	1221717	.	C	T	1847.63	.	AC=12;AF=0.1053;AN=114;BaseQRankSum=0.132;DP=473;Dels=0.00;FS=1.107;HRun=0;HaplotypeScore=0.2958;InbreedingCoeff=0.1362;MQ=58.52;MQ0=0;MQRankSum=-0.162;QD=17.77;ReadPosRankSum=1.073;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1221728	.	G	A	60.11	.	AC=1;AF=0.0089;AN=112;BaseQRankSum=-0.547;DP=393;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3050;InbreedingCoeff=-0.0498;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=15.03;ReadPosRankSum=0.389;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222051	.	A	G	730.01	.	AC=3;AF=0.0259;AN=116;BaseQRankSum=-1.656;DP=566;Dels=0.00;FS=1.481;HRun=4;HaplotypeScore=0.4452;InbreedingCoeff=0.4132;MQ=57.13;MQ0=0;MQRankSum=0.440;QD=29.20;ReadPosRankSum=-0.248;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222267	.	G	C	6009.85	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=-0.365;DP=2056;Dels=0.00;FS=2.228;HRun=5;HaplotypeScore=2.3088;InbreedingCoeff=0.2341;MQ=56.92;MQ0=0;MQRankSum=1.028;QD=15.90;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|7),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R180P|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R180P|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R211P|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R246P|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R344P|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000338555|5/15|possibly_damaging(0.646)|tolerated(0.29)|180/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,missense_variant&NMD_transcript_variant|Gcc/Ccc|A/P|ENSG00000162572|SCNN1D|ENST00000379101|7/17|unknown(0)||313/328|nonsense_mediated_decay|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000325425|5/15|possibly_damaging(0.659)|tolerated(0.22)|246/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000400928|4/14|possibly_damaging(0.646)|tolerated(0.29)|180/638|protein_coding|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000379116|8/18|possibly_damaging(0.659)|tolerated(0.1)|344/802|protein_coding|1
chr1	1222407	.	C	T	341.16	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.879;DP=1311;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0043;InbreedingCoeff=-0.0091;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=17.96;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|5),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|4),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|10),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|5),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|8),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|7);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222598	.	C	T	248.87	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.379;DP=1688;Dels=0.00;FS=2.854;HRun=0;HaplotypeScore=1.2495;InbreedingCoeff=-0.0104;MQ=58.05;MQ0=0;MQRankSum=0.950;QD=9.95;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A246V|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A246V|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A277V|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A312V|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A410V|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000338555|6/15|benign(0.005)|tolerated(0.29)|246/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|8/17|||-/328|nonsense_mediated_decay|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000325425|6/15|benign(0.003)|tolerated(0.29)|312/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162572|SCNN1D|ENST00000379099|1/7|unknown(0)|tolerated(0.05)|38/308|protein_coding|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000400928|5/14|benign(0.005)|tolerated(0.29)|246/638|protein_coding|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000379116|9/18|benign(0.003)|tolerated(0.28)|410/802|protein_coding|1
chr1	1222690	.	C	T	972.9	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.953;DP=1085;Dels=0.00;FS=4.145;HRun=0;HaplotypeScore=2.3729;InbreedingCoeff=-0.0488;MQ=53.44;MQ0=0;MQRankSum=5.040;QD=11.58;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222695	.	G	C	2613.18	.	AC=15;AF=0.1250;AN=120;BaseQRankSum=-2.534;DP=1083;Dels=0.00;FS=12.740;HRun=1;HaplotypeScore=2.6047;InbreedingCoeff=0.2827;MQ=53.52;MQ0=0;MQRankSum=0.965;QD=13.75;ReadPosRankSum=2.874;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222739	.	C	G	156.37	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.552;DP=1353;Dels=0.00;FS=1.709;HRun=0;HaplotypeScore=1.1586;InbreedingCoeff=-0.0117;MQ=56.35;MQ0=0;MQRankSum=-0.469;QD=9.20;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222842	.	C	T	701.62	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.452;DP=3950;Dels=0.00;FS=3.995;HRun=0;HaplotypeScore=2.7986;InbreedingCoeff=-0.0085;MQ=57.76;MQ0=0;MQRankSum=2.038;QD=6.05;ReadPosRankSum=-0.162;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1222958	.	C	T	840.29	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.301;DP=3509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.2081;InbreedingCoeff=-0.0084;MQ=58.04;MQ0=0;MQRankSum=0.486;QD=11.20;ReadPosRankSum=-3.869;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R297C|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R297C|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R328C|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R363C|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R461C|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|9);CSQ=missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000338555|7/15|benign(0.037)|tolerated(0.18)|297/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|9/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000325425|7/15|benign(0.075)|tolerated(0.15)|363/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,synonymous_variant|agC/agT|S|ENSG00000162572|SCNN1D|ENST00000379099|2/7|||88/308|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000400928|6/14|benign(0.037)|tolerated(0.18)|297/638|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000379116|10/18|benign(0.075)|tolerated(0.05)|461/802|protein_coding|1
chr1	1222963	.	C	T	1912.86	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=0.048;DP=3402;DS;Dels=0.00;FS=5.465;HRun=0;HaplotypeScore=2.6679;InbreedingCoeff=-0.0170;MQ=58.00;MQ0=0;MQRankSum=-1.133;QD=11.45;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P298|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P298|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P329|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P364|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P462|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|9);CSQ=synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000338555|7/15|||298/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|9/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000325425|7/15|||364/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000379099|2/7|benign(0.04)|deleterious(0)|90/308|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000400928|6/14|||298/638|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000379116|10/18|||462/802|protein_coding|1
chr1	1223385	.	G	C	1473.29	.	AC=14;AF=0.1250;AN=112;BaseQRankSum=0.369;DP=567;Dels=0.00;FS=6.998;HRun=0;HaplotypeScore=0.6667;InbreedingCoeff=0.0907;MQ=56.62;MQ0=0;MQRankSum=0.356;QD=13.15;ReadPosRankSum=0.501;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E380Q|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E380Q|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E411Q|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E446Q|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E544Q|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000338555|9/15|benign(0.006)|tolerated(0.57)|380/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|11/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000325425|9/15|benign(0.012)|tolerated(0.54)|446/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000379099|3/7|benign(0.047)|tolerated(0.87)|197/308|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000400928|8/14|benign(0.006)|tolerated(0.57)|380/638|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000379116|12/18|benign(0.012)|tolerated(0.47)|544/802|protein_coding|1
chr1	1223465	.	GC	G	883.64	.	AC=11;AF=0.110;AN=100;BaseQRankSum=3.043;DP=292;FS=1.960;HRun=2;HaplotypeScore=26.6146;InbreedingCoeff=0.0959;MQ=54.67;MQ0=0;MQRankSum=1.559;QD=15.24;ReadPosRankSum=1.688;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223570	.	C	T	69.93	.	AC=6;AF=0.065;AN=92;BaseQRankSum=0.235;DP=128;Dels=0.00;FS=2.433;HRun=0;HaplotypeScore=0.0933;InbreedingCoeff=0.2052;MQ=53.21;MQ0=0;MQRankSum=0.920;QD=17.48;ReadPosRankSum=-0.706;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223572	.	C	T	52.77	.	AC=4;AF=0.044;AN=90;BaseQRankSum=1.225;DP=128;Dels=0.00;FS=2.461;HRun=0;HaplotypeScore=0.0513;InbreedingCoeff=0.1293;MQ=53.41;MQ0=0;MQRankSum=1.609;QD=17.59;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223584	.	T	C	172.88	.	AC=12;AF=0.128;AN=94;BaseQRankSum=-0.765;DP=109;Dels=0.00;FS=5.887;HRun=3;HaplotypeScore=0.0818;InbreedingCoeff=0.1717;MQ=52.94;MQ0=0;MQRankSum=-1.734;QD=15.72;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223608	.	T	C	97.92	.	AC=5;AF=0.060;AN=84;BaseQRankSum=0.588;DP=98;Dels=0.00;FS=1.905;HRun=1;HaplotypeScore=0.1871;InbreedingCoeff=0.0757;MQ=49.92;MQ0=0;MQRankSum=0.349;QD=13.99;ReadPosRankSum=1.013;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223626	.	T	C	50.01	.	AC=6;AF=0.081;AN=74;BaseQRankSum=-0.295;DP=80;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.4822;InbreedingCoeff=0.0222;MQ=49.62;MQ0=0;MQRankSum=0.318;QD=7.14;ReadPosRankSum=-0.200;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223660	.	A	T	124.16	.	AC=11;AF=0.183;AN=60;BaseQRankSum=-2.177;DP=70;Dels=0.00;FS=6.078;HRun=0;HaplotypeScore=0.4653;InbreedingCoeff=0.0992;MQ=47.05;MQ0=0;MQRankSum=-3.819;QD=6.21;ReadPosRankSum=-0.646;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223669	.	T	C	30.84	.	AC=2;AF=0.037;AN=54;BaseQRankSum=-0.298;DP=66;Dels=0.00;FS=2.157;HRun=2;HaplotypeScore=0.3049;InbreedingCoeff=-0.1912;MQ=46.88;MQ0=0;MQRankSum=-2.343;QD=3.85;ReadPosRankSum=-1.235;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223721	.	C	T	44.82	.	AC=6;AF=0.150;AN=40;BaseQRankSum=0.689;DP=40;Dels=0.00;FS=2.004;HRun=0;HaplotypeScore=0.3378;InbreedingCoeff=0.0355;MQ=46.71;MQ0=0;MQRankSum=-1.020;QD=4.07;ReadPosRankSum=-1.793;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223741	.	T	C	53.75	.	AC=4;AF=0.105;AN=38;BaseQRankSum=-0.303;DP=42;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3143;InbreedingCoeff=-0.0438;MQ=43.53;MQ0=0;MQRankSum=1.186;QD=4.48;ReadPosRankSum=-0.745;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223754	.	C	T	577.41	.	AC=26;AF=0.619;AN=42;BaseQRankSum=1.117;DP=42;Dels=0.00;FS=5.016;HRun=0;HaplotypeScore=0.4750;InbreedingCoeff=-0.0583;MQ=42.10;MQ0=0;MQRankSum=1.817;QD=16.04;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223759	.	T	C	283.09	.	AC=16;AF=0.400;AN=40;BaseQRankSum=0.405;DP=42;Dels=0.00;FS=20.948;HRun=2;HaplotypeScore=0.3988;InbreedingCoeff=0.0952;MQ=42.43;MQ0=0;MQRankSum=2.503;QD=12.31;ReadPosRankSum=-1.841;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223772	.	C	T	118.73	.	AC=8;AF=0.235;AN=34;BaseQRankSum=0.790;DP=42;Dels=0.02;FS=6.468;HRun=0;HaplotypeScore=0.2464;InbreedingCoeff=-0.0704;MQ=39.82;MQ0=0;MQRankSum=-1.874;QD=6.25;ReadPosRankSum=0.384;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223790	.	C	T	300.88	.	AC=13;AF=0.433;AN=30;BaseQRankSum=1.925;DP=47;Dels=0.04;FS=9.204;HRun=0;HaplotypeScore=0.6820;InbreedingCoeff=-0.0492;MQ=39.36;MQ0=0;MQRankSum=-0.298;QD=10.38;ReadPosRankSum=-3.275;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223795	.	T	C	177.98	.	AC=11;AF=0.324;AN=34;BaseQRankSum=1.748;DP=49;Dels=0.00;FS=11.458;HRun=2;HaplotypeScore=1.0405;InbreedingCoeff=0.1689;MQ=39.01;MQ0=0;MQRankSum=0.452;QD=10.47;ReadPosRankSum=-2.573;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223808	.	C	T	254.07	.	AC=14;AF=0.412;AN=34;BaseQRankSum=0.313;DP=55;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8609;InbreedingCoeff=-0.0598;MQ=39.41;MQ0=0;MQRankSum=-2.458;QD=7.70;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223826	.	T	C	75.31	.	AC=9;AF=0.188;AN=48;BaseQRankSum=-1.209;DP=64;Dels=0.00;FS=1.930;HRun=1;HaplotypeScore=0.5668;InbreedingCoeff=0.0706;MQ=39.48;MQ0=0;MQRankSum=-1.000;QD=4.71;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223831	.	T	C	93.99	.	AC=8;AF=0.174;AN=46;BaseQRankSum=0.839;DP=67;Dels=0.00;FS=1.794;HRun=2;HaplotypeScore=0.6496;InbreedingCoeff=0.1389;MQ=39.56;MQ0=0;MQRankSum=-1.754;QD=7.23;ReadPosRankSum=-1.754;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223846	.	T	C	55.02	.	AC=8;AF=0.143;AN=56;BaseQRankSum=2.634;DP=80;Dels=0.00;FS=6.864;HRun=1;HaplotypeScore=0.8057;InbreedingCoeff=-0.0215;MQ=39.58;MQ0=0;MQRankSum=-2.072;QD=2.50;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223851	.	T	C	109.95	.	AC=9;AF=0.161;AN=56;BaseQRankSum=-1.835;DP=80;Dels=0.00;FS=1.589;HRun=2;HaplotypeScore=0.5852;InbreedingCoeff=-0.0310;MQ=40.14;MQ0=0;MQRankSum=-1.699;QD=3.55;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223864	.	T	C	42.18	.	AC=6;AF=0.094;AN=64;BaseQRankSum=-0.935;DP=85;Dels=0.00;FS=8.168;HRun=1;HaplotypeScore=0.4761;InbreedingCoeff=-0.1023;MQ=39.89;MQ0=0;MQRankSum=-1.619;QD=3.52;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223873	.	T	TCC	58.95	.	AC=5;AF=0.076;AN=66;BaseQRankSum=2.703;DP=91;FS=1.912;HRun=3;HaplotypeScore=29.9562;InbreedingCoeff=-0.1751;MQ=40.59;MQ0=0;MQRankSum=-2.282;QD=3.27;ReadPosRankSum=-0.842;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223887	.	C	T	208.26	.	AC=15;AF=0.242;AN=62;BaseQRankSum=1.248;DP=86;Dels=0.00;FS=1.200;HRun=0;HaplotypeScore=0.4017;InbreedingCoeff=-0.1357;MQ=40.83;MQ0=0;MQRankSum=-2.152;QD=4.84;ReadPosRankSum=0.390;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223900	.	C	T	905.84	.	AC=36;AF=0.643;AN=56;BaseQRankSum=0.938;DP=77;Dels=0.00;FS=0.998;HRun=0;HaplotypeScore=0.6461;InbreedingCoeff=0.0959;MQ=40.99;MQ0=0;MQRankSum=-1.278;QD=14.38;ReadPosRankSum=0.258;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223905	.	T	C	98.29	.	AC=9;AF=0.167;AN=54;BaseQRankSum=-1.946;DP=77;Dels=0.00;FS=3.277;HRun=2;HaplotypeScore=0.5934;InbreedingCoeff=0.1031;MQ=40.55;MQ0=0;MQRankSum=-0.402;QD=5.46;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1223963	.	T	C	128.73	.	AC=10;AF=0.385;AN=26;BaseQRankSum=-0.635;DP=29;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.4996;InbreedingCoeff=-0.0973;MQ=39.99;MQ0=0;MQRankSum=1.102;QD=6.78;ReadPosRankSum=0.301;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225096	.	C	T	123.66	.	AC=9;AF=0.563;AN=16;BaseQRankSum=0.278;DP=16;Dels=0.00;FS=6.990;HRun=0;HaplotypeScore=0.8108;MQ=33.81;MQ0=0;MQRankSum=-1.246;QD=13.74;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225121	.	T	C	79.61	.	AC=9;AF=0.300;AN=30;BaseQRankSum=-0.698;DP=26;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.1615;InbreedingCoeff=0.2471;MQ=30.87;MQ0=0;MQRankSum=-1.397;QD=11.37;ReadPosRankSum=-0.698;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225125	.	TCC	T	136.07	.	AC=9;AF=0.281;AN=32;BaseQRankSum=0.701;DP=25;FS=18.560;HRun=5;HaplotypeScore=19.9646;InbreedingCoeff=-0.0780;MQ=30.60;MQ0=0;MQRankSum=2.186;QD=11.34;ReadPosRankSum=1.196;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225141	.	T	C	32.44	.	AC=5;AF=0.147;AN=34;BaseQRankSum=-0.213;DP=26;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3484;InbreedingCoeff=0.0778;MQ=30.54;MQ0=0;MQRankSum=-1.319;QD=8.11;ReadPosRankSum=-1.149;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225163	.	TCC	T	121.19	.	AC=12;AF=0.353;AN=34;BaseQRankSum=0.452;DP=22;FS=9.260;HRun=5;HaplotypeScore=17.1552;InbreedingCoeff=0.3248;MQ=32.45;MQ0=0;MQRankSum=-1.759;QD=17.31;ReadPosRankSum=0.050;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225174	.	C	T	237.41	.	AC=18;AF=0.643;AN=28;BaseQRankSum=0.648;DP=22;Dels=0.00;FS=2.363;HRun=0;HaplotypeScore=1.0277;InbreedingCoeff=0.3305;MQ=32.25;MQ0=0;MQRankSum=-0.648;QD=26.38;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225239	.	A	T	100.39	.	AC=6;AF=0.500;AN=12;BaseQRankSum=0.550;DP=8;Dels=0.00;FS=3.680;HRun=0;HaplotypeScore=0.0000;MQ=42.45;MQ0=0;MQRankSum=0.550;QD=25.10;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225261	.	T	C	133.06	.	AC=10;AF=0.200;AN=50;BaseQRankSum=0.107;DP=45;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3102;InbreedingCoeff=0.1724;MQ=37.78;MQ0=0;MQRankSum=-0.997;QD=14.78;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225279	.	T	C	111.05	.	AC=13;AF=0.210;AN=62;BaseQRankSum=0.114;DP=66;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.5124;InbreedingCoeff=0.2853;MQ=35.30;MQ0=0;MQRankSum=-1.427;QD=11.10;ReadPosRankSum=-1.376;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225284	.	T	C	256.36	.	AC=13;AF=0.210;AN=62;BaseQRankSum=0.970;DP=68;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.5134;InbreedingCoeff=0.1617;MQ=35.13;MQ0=0;MQRankSum=-1.184;QD=12.82;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225302	.	C	T	193.86	.	AC=15;AF=0.242;AN=62;BaseQRankSum=-1.436;DP=91;Dels=0.00;FS=1.834;HRun=0;HaplotypeScore=1.1816;InbreedingCoeff=0.2195;MQ=33.76;MQ0=0;MQRankSum=0.576;QD=8.43;ReadPosRankSum=1.178;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225312	.	G	A	158.46	.	AC=11;AF=0.172;AN=64;BaseQRankSum=-0.966;DP=93;Dels=0.02;FS=7.390;HRun=0;HaplotypeScore=1.6923;InbreedingCoeff=-0.0065;MQ=33.88;MQ0=0;MQRankSum=-1.247;QD=6.09;ReadPosRankSum=0.910;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225319	.	T	C	311.15	.	AC=16;AF=0.229;AN=70;BaseQRankSum=0.007;DP=97;Dels=0.00;FS=12.678;HRun=1;HaplotypeScore=0.6200;InbreedingCoeff=0.0685;MQ=35.32;MQ0=0;MQRankSum=-2.217;QD=9.15;ReadPosRankSum=2.287;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225325	.	G	A	205.95	.	AC=12;AF=0.176;AN=68;BaseQRankSum=-2.064;DP=103;Dels=0.00;FS=4.701;HRun=0;HaplotypeScore=0.5398;InbreedingCoeff=-0.0183;MQ=36.25;MQ0=0;MQRankSum=-2.585;QD=6.86;ReadPosRankSum=1.419;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225330	.	G	A	109.49	.	AC=8;AF=0.129;AN=62;BaseQRankSum=-2.003;DP=109;Dels=0.00;FS=4.693;HRun=0;HaplotypeScore=0.7228;InbreedingCoeff=-0.1427;MQ=36.47;MQ0=0;MQRankSum=-2.668;QD=3.78;ReadPosRankSum=0.963;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225335	.	T	C	238.86	.	AC=13;AF=0.191;AN=68;BaseQRankSum=-1.449;DP=110;Dels=0.00;FS=7.186;HRun=1;HaplotypeScore=0.5462;InbreedingCoeff=-0.0481;MQ=36.64;MQ0=0;MQRankSum=-2.715;QD=6.46;ReadPosRankSum=-1.710;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225340	.	TC	T	227.19	.	AC=9;AF=0.132;AN=68;BaseQRankSum=5.045;DP=112;FS=7.004;HRun=2;HaplotypeScore=30.7520;InbreedingCoeff=-0.0950;MQ=37.06;MQ0=0;MQRankSum=-2.051;QD=7.33;ReadPosRankSum=-0.410;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225343	.	G	A	137.99	.	AC=9;AF=0.141;AN=64;BaseQRankSum=-2.584;DP=116;Dels=0.01;FS=2.292;HRun=0;HaplotypeScore=0.6542;InbreedingCoeff=-0.1498;MQ=37.81;MQ0=0;MQRankSum=-2.776;QD=4.45;ReadPosRankSum=-2.598;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225350	.	G	C	61.74	.	AC=4;AF=0.065;AN=62;BaseQRankSum=-1.443;DP=105;Dels=0.00;FS=2.393;HRun=5;HaplotypeScore=0.7473;InbreedingCoeff=-0.1912;MQ=39.32;MQ0=0;MQRankSum=-2.240;QD=4.75;ReadPosRankSum=-3.424;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225371	.	C	T	52.17	.	AC=8;AF=0.114;AN=70;BaseQRankSum=0.850;DP=87;Dels=0.00;FS=2.411;HRun=0;HaplotypeScore=0.1882;InbreedingCoeff=0.0721;MQ=42.92;MQ0=0;MQRankSum=-1.185;QD=3.07;ReadPosRankSum=-0.451;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225389	.	C	T	253.01	.	AC=13;AF=0.167;AN=78;BaseQRankSum=1.797;DP=127;Dels=0.00;FS=3.410;HRun=0;HaplotypeScore=0.3513;InbreedingCoeff=0.1116;MQ=41.93;MQ0=0;MQRankSum=-1.326;QD=9.04;ReadPosRankSum=-2.083;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225407	.	T	C	47.15	.	AC=5;AF=0.054;AN=92;BaseQRankSum=-1.004;DP=162;Dels=0.00;FS=2.276;HRun=1;HaplotypeScore=0.5729;InbreedingCoeff=-0.1734;MQ=42.85;MQ0=0;MQRankSum=-1.615;QD=1.68;ReadPosRankSum=2.014;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225425	.	C	T	793.83	.	AC=31;AF=0.337;AN=92;BaseQRankSum=1.412;DP=187;Dels=0.02;FS=6.178;HRun=0;HaplotypeScore=0.4105;InbreedingCoeff=-0.0399;MQ=43.23;MQ0=0;MQRankSum=-4.142;QD=6.56;ReadPosRankSum=0.059;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225443	.	T	C	468.02	.	AC=15;AF=0.163;AN=92;BaseQRankSum=-2.292;DP=235;Dels=0.00;FS=6.953;HRun=1;HaplotypeScore=0.6031;InbreedingCoeff=-0.1815;MQ=43.46;MQ0=0;MQRankSum=-0.753;QD=4.78;ReadPosRankSum=-1.745;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225452	.	T	TCC	330.82	.	AC=10;AF=0.104;AN=96;BaseQRankSum=1.749;DP=270;FS=4.169;HRun=3;HaplotypeScore=57.3296;InbreedingCoeff=-0.1229;MQ=43.34;MQ0=0;MQRankSum=-2.041;QD=5.09;ReadPosRankSum=-2.421;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225461	.	T	C	238.55	.	AC=14;AF=0.1273;AN=110;BaseQRankSum=-0.273;DP=319;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9594;InbreedingCoeff=-0.1003;MQ=43.75;MQ0=0;MQRankSum=-1.815;QD=2.41;ReadPosRankSum=0.946;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225466	.	T	C	184.63	.	AC=11;AF=0.0948;AN=116;BaseQRankSum=-1.477;DP=342;Dels=0.00;FS=1.813;HRun=2;HaplotypeScore=0.9329;InbreedingCoeff=-0.1688;MQ=44.09;MQ0=0;MQRankSum=-2.845;QD=1.85;ReadPosRankSum=-1.214;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225470	.	T	TCC	366.85	.	AC=11;AF=0.0948;AN=116;BaseQRankSum=3.645;DP=363;FS=6.315;HRun=3;HaplotypeScore=61.2598;InbreedingCoeff=-0.1667;MQ=44.55;MQ0=0;MQRankSum=-2.973;QD=4.32;ReadPosRankSum=-1.690;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225479	.	T	C	216.38	.	AC=8;AF=0.0690;AN=116;BaseQRankSum=-0.622;DP=392;Dels=0.00;FS=4.070;HRun=1;HaplotypeScore=1.0837;InbreedingCoeff=0.0601;MQ=45.51;MQ0=0;MQRankSum=-3.522;QD=3.73;ReadPosRankSum=-0.410;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225484	.	T	C	214.92	.	AC=16;AF=0.1379;AN=116;BaseQRankSum=-1.446;DP=412;Dels=0.00;FS=17.524;HRun=2;HaplotypeScore=1.1210;InbreedingCoeff=-0.1039;MQ=45.67;MQ0=0;MQRankSum=-3.630;QD=1.52;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225488	.	T	TCC	73.7	.	AC=6;AF=0.0517;AN=116;BaseQRankSum=3.896;DP=442;FS=2.167;HRun=3;HaplotypeScore=66.4298;InbreedingCoeff=-0.0944;MQ=46.00;MQ0=0;MQRankSum=-2.159;QD=1.23;ReadPosRankSum=-2.147;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225497	.	T	C	35.56	.	AC=5;AF=0.0439;AN=114;BaseQRankSum=-3.665;DP=477;Dels=0.00;FS=3.756;HRun=1;HaplotypeScore=1.4250;InbreedingCoeff=-0.0704;MQ=45.97;MQ0=0;MQRankSum=-2.358;QD=0.73;ReadPosRankSum=0.893;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225502	.	T	C	688.93	.	AC=16;AF=0.1404;AN=114;BaseQRankSum=0.243;DP=497;Dels=0.00;FS=19.856;HRun=2;HaplotypeScore=1.6402;InbreedingCoeff=-0.0754;MQ=46.34;MQ0=0;MQRankSum=-4.470;QD=5.22;ReadPosRankSum=0.940;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225504	.	C	T	33.71	.	AC=3;AF=0.0263;AN=114;BaseQRankSum=-2.542;DP=505;Dels=0.00;FS=4.534;HRun=0;HaplotypeScore=1.6971;InbreedingCoeff=-0.0570;MQ=46.78;MQ0=0;MQRankSum=1.064;QD=1.16;ReadPosRankSum=2.168;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225505	.	G	A	87.65	.	AC=6;AF=0.0526;AN=114;BaseQRankSum=0.061;DP=508;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=1.7900;InbreedingCoeff=-0.0837;MQ=47.10;MQ0=0;MQRankSum=-0.730;QD=1.65;ReadPosRankSum=0.134;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225506	.	TCC	T	120.88	.	AC=8;AF=0.0702;AN=114;BaseQRankSum=7.487;DP=525;FS=3.030;HRun=5;HaplotypeScore=77.2182;InbreedingCoeff=-0.0982;MQ=47.37;MQ0=0;MQRankSum=-3.071;QD=1.92;ReadPosRankSum=-7.075;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225507	.	C	T	63.16	.	AC=5;AF=0.0439;AN=114;BaseQRankSum=0.195;DP=525;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=2.6528;InbreedingCoeff=-0.0729;MQ=47.37;MQ0=0;MQRankSum=-0.118;QD=1.58;ReadPosRankSum=1.001;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225512	.	G	A	59.61	.	AC=5;AF=0.0431;AN=116;BaseQRankSum=0.671;DP=562;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=2.9722;InbreedingCoeff=-0.0588;MQ=48.31;MQ0=0;MQRankSum=-3.136;QD=1.24;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225517	.	T	C	31.29	.	AC=10;AF=0.0862;AN=116;BaseQRankSum=-0.543;DP=597;Dels=0.00;FS=8.293;HRun=1;HaplotypeScore=2.0472;InbreedingCoeff=0.0340;MQ=48.76;MQ0=0;MQRankSum=-2.154;QD=0.33;ReadPosRankSum=-1.343;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225522	.	T	C	265.0	.	AC=14;AF=0.1207;AN=116;BaseQRankSum=-0.678;DP=629;Dels=0.00;FS=97.747;HRun=2;HaplotypeScore=1.7833;InbreedingCoeff=-0.1442;MQ=49.06;MQ0=0;MQRankSum=-5.490;QD=1.44;ReadPosRankSum=-0.496;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225526	.	T	TCC	411.2	.	AC=10;AF=0.0862;AN=116;BaseQRankSum=4.261;DP=667;FS=14.873;HRun=3;HaplotypeScore=89.4036;InbreedingCoeff=-0.1134;MQ=49.86;MQ0=0;MQRankSum=-3.366;QD=3.29;ReadPosRankSum=-3.904;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225535	.	T	C	848.26	.	AC=10;AF=0.0862;AN=116;BaseQRankSum=-1.442;DP=750;Dels=0.00;FS=4.302;HRun=1;HaplotypeScore=1.3486;InbreedingCoeff=-0.1129;MQ=50.86;MQ0=0;MQRankSum=1.251;QD=5.89;ReadPosRankSum=-1.457;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225540	.	T	C	45.1	.	AC=3;AF=0.0259;AN=116;BaseQRankSum=-1.838;DP=782;Dels=0.00;FS=14.682;HRun=2;HaplotypeScore=1.0795;InbreedingCoeff=-0.0391;MQ=51.27;MQ0=0;MQRankSum=-3.072;QD=2.37;ReadPosRankSum=-2.538;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225543	.	G	C	72.05	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=1.703;DP=821;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.7205;InbreedingCoeff=-0.0188;MQ=51.72;MQ0=0;MQRankSum=1.023;QD=3.79;ReadPosRankSum=-1.656;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225544	.	T	TCC	104.04	.	AC=3;AF=0.0263;AN=114;BaseQRankSum=5.030;DP=839;FS=11.849;HRun=3;HaplotypeScore=111.7887;InbreedingCoeff=-0.0353;MQ=51.88;MQ0=0;MQRankSum=-4.162;QD=3.15;ReadPosRankSum=-3.869;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225553	.	C	T	5273.44	.	AC=32;AF=0.2807;AN=114;BaseQRankSum=1.380;DP=911;Dels=0.00;FS=0.497;HRun=0;HaplotypeScore=1.8119;InbreedingCoeff=-0.1881;MQ=52.16;MQ0=0;MQRankSum=2.230;QD=11.39;ReadPosRankSum=-0.044;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225558	.	T	C	207.02	.	AC=1;AF=0.0086;AN=116;BaseQRankSum=0.020;DP=961;Dels=0.00;FS=8.305;HRun=2;HaplotypeScore=1.2090;InbreedingCoeff=-0.0183;MQ=52.59;MQ0=0;MQRankSum=-0.514;QD=12.94;ReadPosRankSum=1.515;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225562	.	T	TCC	147.67	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=3.446;DP=1028;FS=15.375;HRun=3;HaplotypeScore=125.4377;InbreedingCoeff=0.2845;MQ=53.39;MQ0=0;MQRankSum=-2.465;QD=3.14;ReadPosRankSum=-3.790;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225571	.	C	T	5357.09	.	AC=38;AF=0.3167;AN=120;BaseQRankSum=-0.715;DP=1167;Dels=0.00;FS=5.301;HRun=0;HaplotypeScore=2.7736;InbreedingCoeff=0.0326;MQ=54.57;MQ0=0;MQRankSum=-3.297;QD=10.50;ReadPosRankSum=-0.766;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225576	.	T	C	4461.84	.	AC=22;AF=0.1833;AN=120;BaseQRankSum=2.082;DP=1262;Dels=0.00;FS=21.631;HRun=2;HaplotypeScore=2.8144;InbreedingCoeff=0.1776;MQ=54.78;MQ0=0;MQRankSum=0.294;QD=13.48;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225579	.	G	C	1702.39	.	AC=10;AF=0.0833;AN=120;BaseQRankSum=1.093;DP=1332;Dels=0.00;FS=11.111;HRun=2;HaplotypeScore=2.9711;InbreedingCoeff=0.0608;MQ=55.00;MQ0=0;MQRankSum=0.576;QD=11.74;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225597	.	G	A	764.88	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.619;DP=1769;Dels=0.00;FS=3.258;HRun=0;HaplotypeScore=1.9881;InbreedingCoeff=-0.0171;MQ=55.96;MQ0=0;MQRankSum=3.394;QD=15.61;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225604	.	A	G	288.23	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.165;DP=1945;Dels=0.00;FS=50.790;HRun=0;HaplotypeScore=2.6125;InbreedingCoeff=-0.0085;MQ=56.12;MQ0=0;MQRankSum=-4.687;QD=13.10;ReadPosRankSum=-3.197;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225612	.	G	A	8878.59	.	AC=25;AF=0.2083;AN=120;BaseQRankSum=-2.436;DP=2093;Dels=0.00;FS=21.815;HRun=0;HaplotypeScore=1.7123;InbreedingCoeff=0.1407;MQ=56.18;MQ0=0;MQRankSum=1.022;QD=13.60;ReadPosRankSum=-1.768;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225641	.	C	A	16235.21	.	AC=27;AF=0.2250;AN=120;BaseQRankSum=-0.237;DP=2629;Dels=0.00;FS=1.703;HRun=0;HaplotypeScore=1.7639;InbreedingCoeff=0.3777;MQ=56.48;MQ0=0;MQRankSum=2.792;QD=20.32;ReadPosRankSum=2.777;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225804	.	A	G	641.95	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.178;DP=3135;Dels=0.00;FS=4.019;HRun=0;HaplotypeScore=3.7390;InbreedingCoeff=-0.0085;MQ=57.48;MQ0=0;MQRankSum=2.112;QD=13.10;ReadPosRankSum=1.189;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225810	.	C	CGG	5006.7	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=1.861;DP=3131;FS=0.360;HRun=6;HaplotypeScore=237.1014;InbreedingCoeff=0.6361;MQ=57.43;MQ0=0;MQRankSum=-0.361;QD=33.60;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225824	.	G	A	1475.6	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.326;DP=3390;Dels=0.00;FS=1.074;HRun=1;HaplotypeScore=2.3868;InbreedingCoeff=-0.0086;MQ=57.43;MQ0=0;MQRankSum=2.353;QD=12.20;ReadPosRankSum=-2.766;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225945	.	G	C	3949.71	.	AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.101;DP=3777;Dels=0.00;FS=22.292;HRun=0;HaplotypeScore=4.0017;InbreedingCoeff=0.6569;MQ=57.83;MQ0=0;MQRankSum=-0.665;QD=25.32;ReadPosRankSum=2.508;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|11),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|10),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|16),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|11),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|14),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|13);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1225959	.	C	G	25993.98	.	AC=36;AF=0.3000;AN=120;BaseQRankSum=1.580;DP=3659;Dels=0.00;FS=21.530;HRun=2;HaplotypeScore=2.4662;InbreedingCoeff=0.2055;MQ=57.98;MQ0=0;MQRankSum=1.714;QD=17.82;ReadPosRankSum=0.723;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|11),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|10),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|16),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|11),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|14),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|13);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226063	.	G	A	1804.82	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.166;DP=2009;Dels=0.00;FS=1.053;HRun=0;HaplotypeScore=1.1275;InbreedingCoeff=-0.0436;MQ=58.53;MQ0=0;MQRankSum=0.440;QD=9.35;ReadPosRankSum=-0.405;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A472T|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A472T|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A503T|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A538T|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A636T|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000338555|12/15|benign(0.168)|tolerated(0.19)|472/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|14/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000325425|12/15|benign(0.109)|tolerated(0.39)|538/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000379099|6/7|benign(0.297)|tolerated(0.13)|289/308|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000400928|11/14|benign(0.168)|tolerated(0.19)|472/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000379116|15/18|benign(0.109)|tolerated(0.29)|636/802|protein_coding|1
chr1	1226102	.	G	A	4016.45	.	AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.245;DP=1541;Dels=0.00;FS=2.281;HRun=0;HaplotypeScore=1.2555;InbreedingCoeff=0.2951;MQ=58.35;MQ0=0;MQRankSum=0.176;QD=16.67;ReadPosRankSum=2.379;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226139	.	G	A	53.13	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.435;DP=1276;Dels=0.00;FS=8.998;HRun=1;HaplotypeScore=0.7541;InbreedingCoeff=-0.0093;MQ=58.09;MQ0=0;MQRankSum=-1.197;QD=2.95;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226217	.	A	G	385.18	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.713;DP=1445;Dels=0.00;FS=1.054;HRun=0;HaplotypeScore=1.4065;InbreedingCoeff=-0.0114;MQ=58.08;MQ0=0;MQRankSum=0.322;QD=12.84;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226221	.	A	G	12961.74	.	AC=36;AF=0.3000;AN=120;BaseQRankSum=0.407;DP=1473;Dels=0.00;FS=8.750;HRun=2;HaplotypeScore=1.9078;InbreedingCoeff=0.3380;MQ=58.10;MQ0=0;MQRankSum=0.672;QD=20.00;ReadPosRankSum=-0.137;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226231	.	G	A	1060.58	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=0.134;DP=1522;Dels=0.00;FS=3.076;HRun=0;HaplotypeScore=2.2801;InbreedingCoeff=-0.0375;MQ=58.05;MQ0=0;MQRankSum=1.141;QD=13.26;ReadPosRankSum=0.602;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226233	.	G	A	432.75	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.014;DP=1544;Dels=0.00;FS=11.621;HRun=0;HaplotypeScore=1.7754;InbreedingCoeff=-0.0115;MQ=58.14;MQ0=0;MQRankSum=1.437;QD=9.21;ReadPosRankSum=-0.335;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226246	.	C	T	658.46	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.957;DP=1671;Dels=0.00;FS=1.750;HRun=0;HaplotypeScore=1.4315;InbreedingCoeff=-0.0192;MQ=58.19;MQ0=0;MQRankSum=1.240;QD=9.98;ReadPosRankSum=-0.155;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226267	.	G	A	198.26	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.326;DP=1848;Dels=0.00;FS=1.356;HRun=0;HaplotypeScore=0.8439;InbreedingCoeff=-0.0108;MQ=58.43;MQ0=0;MQRankSum=-0.958;QD=8.62;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226292	.	G	A	2311.15	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.197;DP=2007;Dels=0.00;FS=0.860;HRun=0;HaplotypeScore=1.1337;InbreedingCoeff=-0.0381;MQ=58.08;MQ0=0;MQRankSum=0.237;QD=11.79;ReadPosRankSum=1.765;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T481|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T481|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T512|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T547|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T645|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000338555|13/15|||481/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|15/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000325425|13/15|||547/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000379099|7/7|||298/308|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000400928|12/14|||481/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000379116|16/18|||645/802|protein_coding|1
chr1	1226348	.	C	G	14565.59	.	AC=27;AF=0.2250;AN=120;BaseQRankSum=-4.148;DP=2185;Dels=0.00;FS=12.103;HRun=0;HaplotypeScore=3.8823;InbreedingCoeff=0.3031;MQ=57.72;MQ0=0;MQRankSum=-0.548;QD=19.76;ReadPosRankSum=2.686;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226350	.	C	T	913.84	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.958;DP=2174;Dels=0.00;FS=1.375;HRun=0;HaplotypeScore=3.4324;InbreedingCoeff=-0.0112;MQ=57.70;MQ0=0;MQRankSum=0.687;QD=12.52;ReadPosRankSum=2.553;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226418	.	C	T	612.71	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=0.522;DP=1764;Dels=0.00;FS=13.559;HRun=0;HaplotypeScore=1.3627;InbreedingCoeff=-0.0097;MQ=57.73;MQ0=0;MQRankSum=0.737;QD=13.93;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226419	.	G	A	122.55	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.320;DP=1752;Dels=0.00;FS=6.374;HRun=0;HaplotypeScore=1.2212;InbreedingCoeff=-0.0099;MQ=57.75;MQ0=0;MQRankSum=0.393;QD=5.33;ReadPosRankSum=0.165;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226423	.	T	C	2109.1	.	AC=4;AF=0.0333;AN=120;BaseQRankSum=1.172;DP=1776;Dels=0.00;FS=0.924;HRun=3;HaplotypeScore=1.1033;InbreedingCoeff=0.4687;MQ=57.78;MQ0=0;MQRankSum=3.304;QD=24.24;ReadPosRankSum=0.918;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226512	.	G	A	620.19	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=1.007;DP=1562;Dels=0.00;FS=9.380;HRun=0;HaplotypeScore=0.9448;InbreedingCoeff=-0.0116;MQ=58.77;MQ0=0;MQRankSum=0.069;QD=24.81;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V518M|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V518M|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V549M|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V584M|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V682M|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|16);CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000338555|14/15|benign(0.109)|tolerated(0.11)|518/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|16/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000325425|14/15|benign(0.036)|tolerated(0.12)|584/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000400928|13/14|benign(0.109)|tolerated(0.11)|518/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000379116|17/18|benign(0.036)|tolerated(0.1)|682/802|protein_coding|1
chr1	1226539	.	C	T	817.48	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.085;DP=1317;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6593;InbreedingCoeff=-0.0489;MQ=58.71;MQ0=0;MQRankSum=0.576;QD=13.62;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|14),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|13),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|19),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|14),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|17),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|16);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1
chr1	1226651	.	G	C	418.81	.	AC=5;AF=0.0417;AN=120;BaseQRankSum=2.115;DP=667;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3223;InbreedingCoeff=-0.0562;MQ=58.20;MQ0=0;MQRankSum=0.758;QD=9.74;ReadPosRankSum=-0.561;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S526|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S526|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S557|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S592|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S690|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|17);CSQ=synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|||526/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|17/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|||592/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|||526/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|||690/802|protein_coding|1
chr1	1226690	.	C	T	282.98	.	AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.735;DP=758;Dels=0.00;FS=19.978;HRun=0;HaplotypeScore=0.3775;InbreedingCoeff=-0.0239;MQ=58.31;MQ0=0;MQRankSum=0.192;QD=12.30;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S539|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S539|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S570|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S605|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S703|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|17);CSQ=synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|||539/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|17/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|||605/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|||539/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|||703/802|protein_coding|1
chr1	1226757	.	G	A	1577.2	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=-2.078;DP=939;Dels=0.00;FS=1.648;HRun=0;HaplotypeScore=0.5032;InbreedingCoeff=-0.1091;MQ=57.89;MQ0=0;MQRankSum=0.038;QD=8.76;ReadPosRankSum=0.677;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G562S|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G562S|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G593S|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G628S|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G726S|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.125)|tolerated(0.39)|562/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.276)|tolerated(0.4)|628/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.125)|tolerated(0.39)|562/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.276)|tolerated(0.4)|726/802|protein_coding|1
chr1	1226851	.	C	T	188.21	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.990;DP=1115;Dels=0.00;FS=5.214;HRun=0;HaplotypeScore=0.5651;InbreedingCoeff=-0.0104;MQ=58.68;MQ0=0;MQRankSum=-1.264;QD=9.41;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P593L|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P593L|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P624L|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P659L|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P757L|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.007)|deleterious(0.05)|593/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.005)|tolerated(0.09)|659/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.007)|deleterious(0.05)|593/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.005)|deleterious(0.02)|757/802|protein_coding|1
chr1	1226889	.	G	A	2836.8	.	AC=12;AF=0.1000;AN=120;BaseQRankSum=-2.929;DP=1114;Dels=0.00;FS=6.315;HRun=0;HaplotypeScore=0.3672;InbreedingCoeff=-0.1141;MQ=58.73;MQ0=0;MQRankSum=0.148;QD=15.76;ReadPosRankSum=0.535;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G606R|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G606R|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G637R|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G672R|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G770R|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.159)|tolerated(0.42)|606/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.001)|tolerated(0.38)|672/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.159)|tolerated(0.42)|606/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.001)|tolerated(0.08)|770/802|protein_coding|1
chr1	1226971	.	T	C	63.36	.	AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.160;DP=1268;Dels=0.00;FS=4.729;HRun=4;HaplotypeScore=0.4672;InbreedingCoeff=-0.0189;MQ=58.51;MQ0=0;MQRankSum=1.085;QD=3.73;ReadPosRankSum=-0.628;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L633P|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L633P|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L664P|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L699P|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L797P|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.02)|tolerated(0.18)|633/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.189)|tolerated(0.21)|699/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.02)|tolerated(0.18)|633/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.189)|deleterious(0.04)|797/802|protein_coding|1
chr1	1227042	.	G	A	57.76	.	AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.393;DP=957;Dels=0.00;FS=2.494;HRun=0;HaplotypeScore=0.5259;InbreedingCoeff=-0.0359;MQ=58.61;MQ0=0;MQRankSum=0.096;QD=14.44;ReadPosRankSum=2.314;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|15),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|14),UTR_3_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|20),UTR_3_PRIME(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|15),UTR_3_PRIME(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|18);CSQ=3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|15/15|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000325425|15/15|||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|14/14|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000379116|18/18|||-/802|protein_coding|1
chr1	1227196	.	A	G	1166.6	.	AC=2;AF=0.024;AN=82;BaseQRankSum=1.195;DP=1062;Dels=0.00;FS=10.378;HRun=6;HaplotypeScore=1.5050;InbreedingCoeff=-0.0572;MQ=57.57;MQ0=0;MQRankSum=-0.308;QD=10.42;ReadPosRankSum=0.286;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|15),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|14),UTR_3_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|20),UTR_3_PRIME(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|15),UTR_3_PRIME(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|18);CSQ=3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|15/15|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000325425|15/15|||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|14/14|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000379116|18/18|||-/802|protein_coding|1