##fileformat=VCFv4.2
##SnpEffVersion="4.3r (build 2017-09-06 16:41), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh38.p7.RefSeq /var/runs/2018-01-29_21-14-19_GM1__MTgzNDgyMz/germline-variants-all.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.6+htslib-1.6
##samtoolsCommand=samtools mpileup -v -u -B -t DP -f /var/references/ucsc/180092/hg38/sequences/full.fa /var/runs/2018-01-29_21-14-19_GM1__MTgzNDgyMz/mapped-sorted-mkdup.bam
##reference=file:///var/references/ucsc/180092/hg38/sequences/full.fa
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##contig=<ID=chr21_KI270873v1_alt,length=143900>
##contig=<ID=chr21_KI270874v1_alt,length=166743>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chr22_GL383582v2_alt,length=162811>
##contig=<ID=chr22_GL383583v2_alt,length=96924>
##contig=<ID=chr22_KB663609v1_alt,length=74013>
##contig=<ID=chr22_KI270731v1_random,length=150754>
##contig=<ID=chr22_KI270732v1_random,length=41543>
##contig=<ID=chr22_KI270733v1_random,length=179772>
##contig=<ID=chr22_KI270734v1_random,length=165050>
##contig=<ID=chr22_KI270735v1_random,length=42811>
##contig=<ID=chr22_KI270736v1_random,length=181920>
##contig=<ID=chr22_KI270737v1_random,length=103838>
##contig=<ID=chr22_KI270738v1_random,length=99375>
##contig=<ID=chr22_KI270739v1_random,length=73985>
##contig=<ID=chr22_KI270875v1_alt,length=259914>
##contig=<ID=chr22_KI270876v1_alt,length=263666>
##contig=<ID=chr22_KI270877v1_alt,length=101331>
##contig=<ID=chr22_KI270878v1_alt,length=186262>
##contig=<ID=chr22_KI270879v1_alt,length=304135>
##contig=<ID=chr22_KI270928v1_alt,length=176103>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrX_KI270880v1_alt,length=284869>
##contig=<ID=chrX_KI270881v1_alt,length=144206>
##contig=<ID=chrX_KI270913v1_alt,length=274009>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrY_KI270740v1_random,length=37240>
##contig=<ID=chrM,length=16569>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chrUn_GL000226v1,length=15008>
##contig=<ID=chrUn_KI270302v1,length=2274>
##contig=<ID=chrUn_KI270303v1,length=1942>
##contig=<ID=chrUn_KI270304v1,length=2165>
##contig=<ID=chrUn_KI270305v1,length=1472>
##contig=<ID=chrUn_KI270310v1,length=1201>
##contig=<ID=chrUn_KI270311v1,length=12399>
##contig=<ID=chrUn_KI270312v1,length=998>
##contig=<ID=chrUn_KI270315v1,length=2276>
##contig=<ID=chrUn_KI270316v1,length=1444>
##contig=<ID=chrUn_KI270317v1,length=37690>
##contig=<ID=chrUn_KI270320v1,length=4416>
##contig=<ID=chrUn_KI270322v1,length=21476>
##contig=<ID=chrUn_KI270329v1,length=1040>
##contig=<ID=chrUn_KI270330v1,length=1652>
##contig=<ID=chrUn_KI270333v1,length=2699>
##contig=<ID=chrUn_KI270334v1,length=1368>
##contig=<ID=chrUn_KI270335v1,length=1048>
##contig=<ID=chrUn_KI270336v1,length=1026>
##contig=<ID=chrUn_KI270337v1,length=1121>
##contig=<ID=chrUn_KI270338v1,length=1428>
##contig=<ID=chrUn_KI270340v1,length=1428>
##contig=<ID=chrUn_KI270362v1,length=3530>
##contig=<ID=chrUn_KI270363v1,length=1803>
##contig=<ID=chrUn_KI270364v1,length=2855>
##contig=<ID=chrUn_KI270366v1,length=8320>
##contig=<ID=chrUn_KI270371v1,length=2805>
##contig=<ID=chrUn_KI270372v1,length=1650>
##contig=<ID=chrUn_KI270373v1,length=1451>
##contig=<ID=chrUn_KI270374v1,length=2656>
##contig=<ID=chrUn_KI270375v1,length=2378>
##contig=<ID=chrUn_KI270376v1,length=1136>
##contig=<ID=chrUn_KI270378v1,length=1048>
##contig=<ID=chrUn_KI270379v1,length=1045>
##contig=<ID=chrUn_KI270381v1,length=1930>
##contig=<ID=chrUn_KI270382v1,length=4215>
##contig=<ID=chrUn_KI270383v1,length=1750>
##contig=<ID=chrUn_KI270384v1,length=1658>
##contig=<ID=chrUn_KI270385v1,length=990>
##contig=<ID=chrUn_KI270386v1,length=1788>
##contig=<ID=chrUn_KI270387v1,length=1537>
##contig=<ID=chrUn_KI270388v1,length=1216>
##contig=<ID=chrUn_KI270389v1,length=1298>
##contig=<ID=chrUn_KI270390v1,length=2387>
##contig=<ID=chrUn_KI270391v1,length=1484>
##contig=<ID=chrUn_KI270392v1,length=971>
##contig=<ID=chrUn_KI270393v1,length=1308>
##contig=<ID=chrUn_KI270394v1,length=970>
##contig=<ID=chrUn_KI270395v1,length=1143>
##contig=<ID=chrUn_KI270396v1,length=1880>
##contig=<ID=chrUn_KI270411v1,length=2646>
##contig=<ID=chrUn_KI270412v1,length=1179>
##contig=<ID=chrUn_KI270414v1,length=2489>
##contig=<ID=chrUn_KI270417v1,length=2043>
##contig=<ID=chrUn_KI270418v1,length=2145>
##contig=<ID=chrUn_KI270419v1,length=1029>
##contig=<ID=chrUn_KI270420v1,length=2321>
##contig=<ID=chrUn_KI270422v1,length=1445>
##contig=<ID=chrUn_KI270423v1,length=981>
##contig=<ID=chrUn_KI270424v1,length=2140>
##contig=<ID=chrUn_KI270425v1,length=1884>
##contig=<ID=chrUn_KI270429v1,length=1361>
##contig=<ID=chrUn_KI270435v1,length=92983>
##contig=<ID=chrUn_KI270438v1,length=112505>
##contig=<ID=chrUn_KI270442v1,length=392061>
##contig=<ID=chrUn_KI270448v1,length=7992>
##contig=<ID=chrUn_KI270465v1,length=1774>
##contig=<ID=chrUn_KI270466v1,length=1233>
##contig=<ID=chrUn_KI270467v1,length=3920>
##contig=<ID=chrUn_KI270468v1,length=4055>
##contig=<ID=chrUn_KI270507v1,length=5353>
##contig=<ID=chrUn_KI270508v1,length=1951>
##contig=<ID=chrUn_KI270509v1,length=2318>
##contig=<ID=chrUn_KI270510v1,length=2415>
##contig=<ID=chrUn_KI270511v1,length=8127>
##contig=<ID=chrUn_KI270512v1,length=22689>
##contig=<ID=chrUn_KI270515v1,length=6361>
##contig=<ID=chrUn_KI270516v1,length=1300>
##contig=<ID=chrUn_KI270517v1,length=3253>
##contig=<ID=chrUn_KI270518v1,length=2186>
##contig=<ID=chrUn_KI270519v1,length=138126>
##contig=<ID=chrUn_KI270521v1,length=7642>
##contig=<ID=chrUn_KI270522v1,length=5674>
##contig=<ID=chrUn_KI270528v1,length=2983>
##contig=<ID=chrUn_KI270529v1,length=1899>
##contig=<ID=chrUn_KI270530v1,length=2168>
##contig=<ID=chrUn_KI270538v1,length=91309>
##contig=<ID=chrUn_KI270539v1,length=993>
##contig=<ID=chrUn_KI270544v1,length=1202>
##contig=<ID=chrUn_KI270548v1,length=1599>
##contig=<ID=chrUn_KI270579v1,length=31033>
##contig=<ID=chrUn_KI270580v1,length=1553>
##contig=<ID=chrUn_KI270581v1,length=7046>
##contig=<ID=chrUn_KI270582v1,length=6504>
##contig=<ID=chrUn_KI270583v1,length=1400>
##contig=<ID=chrUn_KI270584v1,length=4513>
##contig=<ID=chrUn_KI270587v1,length=2969>
##contig=<ID=chrUn_KI270588v1,length=6158>
##contig=<ID=chrUn_KI270589v1,length=44474>
##contig=<ID=chrUn_KI270590v1,length=4685>
##contig=<ID=chrUn_KI270591v1,length=5796>
##contig=<ID=chrUn_KI270593v1,length=3041>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chrUn_KI270745v1,length=41891>
##contig=<ID=chrUn_KI270746v1,length=66486>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chrUn_KI270748v1,length=93321>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270752v1,length=27745>
##contig=<ID=chrUn_KI270753v1,length=62944>
##contig=<ID=chrUn_KI270754v1,length=40191>
##contig=<ID=chrUn_KI270755v1,length=36723>
##contig=<ID=chrUn_KI270756v1,length=79590>
##contig=<ID=chrUn_KI270757v1,length=71251>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version=3>
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##bcftools_callVersion=1.6+htslib-1.6
##bcftools_callCommand=call -c -v -; Date=Mon Jan 29 22:33:02 2018
##SnpSiftVersion="SnpSift 4.3r (build 2017-09-06 16:41), by Pablo Cingolani"
##SnpSiftCmd=""
##INFO=<ID=CDA,Number=0,Type=Flag,Description="Variation is interrogated in a clinical diagnostic assay">
##INFO=<ID=OTH,Number=0,Type=Flag,Description="Has other variant with exactly the same set of mapped positions on NCBI refernce assembly.">
##INFO=<ID=S3D,Number=0,Type=Flag,Description="Has 3D structure - SNP3D table">
##INFO=<ID=WTD,Number=0,Type=Flag,Description="Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory">
##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">
##INFO=<ID=SLO,Number=0,Type=Flag,Description="Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out">
##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44">
##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13">
##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15">
##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41">
##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42">
##INFO=<ID=G5A,Number=0,Type=Flag,Description=">5% minor allele frequency in each and all populations">
##INFO=<ID=COMMON,Number=1,Type=Integer,Description="RS is a common SNP.  A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency.">
##INFO=<ID=RS,Number=1,Type=Integer,Description="dbSNP ID (i.e. rs number)">
##INFO=<ID=RV,Number=0,Type=Flag,Description="RS orientation is reversed">
##INFO=<ID=TPA,Number=0,Type=Flag,Description="Provisional Third Party Annotation(TPA) (currently rs from PHARMGKB who will give phenotype data)">
##INFO=<ID=CFL,Number=0,Type=Flag,Description="Has Assembly conflict. This is for weight 1 and 2 variant that maps to different chromosomes on different assemblies.">
##INFO=<ID=GNO,Number=0,Type=Flag,Description="Genotypes available. The variant has individual genotype (in SubInd table).">
##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the variant has 2+ minor allele count based on frequency or genotype data.">
##INFO=<ID=ASP,Number=0,Type=Flag,Description="Is Assembly specific. This is set if the variant only maps to one assembly">
##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73">
##INFO=<ID=REF,Number=0,Type=Flag,Description="Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8">
##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53">
##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55">
##INFO=<ID=TOPMED,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.">
##INFO=<ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
##INFO=<ID=MTP,Number=0,Type=Flag,Description="Microattribution/third-party annotation(TPA:GWAS,PAGE)">
##INFO=<ID=LSD,Number=0,Type=Flag,Description="Submitted from a locus-specific database">
##INFO=<ID=NOC,Number=0,Type=Flag,Description="Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.">
##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75">
##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3">
##INFO=<ID=KGPhase3,Number=0,Type=Flag,Description="1000 Genome phase 3">
##INFO=<ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
##INFO=<ID=MUT,Number=0,Type=Flag,Description="Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources">
##INFO=<ID=KGPhase1,Number=0,Type=Flag,Description="1000 Genome phase 1 (incl. June Interim phase 1)">
##INFO=<ID=NOV,Number=0,Type=Flag,Description="Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common.">
##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property.  Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf">
##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6">
##INFO=<ID=G5,Number=0,Type=Flag,Description=">5% minor allele frequency in 1+ populations">
##INFO=<ID=OM,Number=0,Type=Flag,Description="Has OMIM/OMIA">
##INFO=<ID=PMC,Number=0,Type=Flag,Description="Links exist to PubMed Central article">
##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
##INFO=<ID=RSPOS,Number=1,Type=Integer,Description="Chr position reported in dbSNP">
##INFO=<ID=HD,Number=0,Type=Flag,Description="Marker is on high density genotyping kit (50K density or greater).  The variant may have phenotype associations present in dbGaP.">
##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
##source_20180319.1=vcf-merge(v0.1.14-12-gcdb80b8) germline-variants-all-fx.vcf.gz germline-variants-all-dbsnp.vcf.gz
##sourceFiles_20180319.1=0:germline-variants-all-fx.vcf.gz,1:germline-variants-all-dbsnp.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002
chr1	16760749	.	ACCCCC	ACCCC	59.68	.	AC1=1;AC=2;AF1=0.526316;AN=4;ANN=ACCCC|frameshift_variant|HIGH|MST1L|MST1L|transcript|NM_001271733.1|protein_coding|3/15|c.335delG|p.Tyr114fs|335/4668|335/2070|112/689||;DP4=6,8,22,6;DP=58;FQ=-24.5401;IDV=18;IMF=0.62069;INDEL;LOF=(MST1L|MST1L|1|1.00);MQ0F=0.241379;MQ=37;MQSB=0.112836;PV4=0.156364,0.491785,1,1;SF=0,1;SGB=-0.686358;VDB=0.804531	GT:DP:PL	0/1:21:97,0,10	0/1:21:97,0,10
chr14	20060289	.	TCATAGATTTGCTCACTGACCA	TCA	217.47	.	AC1=1;AC=2;AF1=0.5;AN=4;ANN=TCA|frameshift_variant|HIGH|OR4L1|OR4L1|transcript|NM_001004717.1|protein_coding|1/1|c.248_266delTAGATTTGCTCACTGACCA|p.Ile83fs|248/939|248/939|83/312||;DP4=32,78,18,54;DP=228;FQ=217.468;IDV=35;IMF=0.307018;INDEL;LOF=(OR4L1|OR4L1|1|1.00);MQ0F=0;MQ=60;MQSB=1;PV4=0.8111,1,1,1;SF=0,1;SGB=-0.693139;VDB=0.0361447	GT:PL:DP	0/1:255,0,255:91	0/1:255,0,255:91
chr7	100064888	.	GTAGTTA	GTA	217.47	.	AC1=1;AC=2;AF1=0.5;AN=4;ANN=GTA|frameshift_variant|HIGH|ZNF3|ZNF3|transcript|NM_001318137.1|protein_coding|4/4|c.182_185delTAAC|p.Thr62fs|368/1412|182/288|61/95||,GTA|frameshift_variant|HIGH|ZNF3|ZNF3|transcript|NM_017715.3|protein_coding|6/6|c.290_293delTAAC|p.Thr98fs|620/1664|290/396|97/131||,GTA|3_prime_UTR_variant|MODIFIER|ZSCAN21|ZSCAN21|transcript|NM_145914.2|protein_coding|4/4|c.*274_*277delGTTA|||||274|,GTA|3_prime_UTR_variant|MODIFIER|ZSCAN21|ZSCAN21|transcript|XM_017012585.1|protein_coding|5/5|c.*240_*243delGTTA|||||240|,GTA|3_prime_UTR_variant|MODIFIER|ZSCAN21|ZSCAN21|transcript|XM_006716113.3|protein_coding|4/4|c.*274_*277delGTTA|||||274|,GTA|3_prime_UTR_variant|MODIFIER|ZSCAN21|ZSCAN21|transcript|XM_005250568.4|protein_coding|5/5|c.*274_*277delGTTA|||||274|,GTA|3_prime_UTR_variant|MODIFIER|ZSCAN21|ZSCAN21|transcript|XM_017012584.1|protein_coding|5/5|c.*274_*277delGTTA|||||274|;DP4=12,30,6,10;DP=70;FQ=217.468;IDV=8;IMF=0.228571;INDEL;LOF=(ZNF3|ZNF3|13|0.15);MQ0F=0;MQ=60;MQSB=1;PV4=0.674904,0.163769,1,0.171083;SF=0,1;SGB=-0.651104;VDB=0.0254548	GT:PL:DP	0/1:255,0,255:29	0/1:255,0,255:29
chr15	40407805	.	GTTTT	GTT	54.47	.	AC1=1;AC=2;AF1=0.5;AN=4;ANN=GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022149.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|358/1798|326/1551|109/516||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022158.1|protein_coding|2/8|c.326_327delTT|p.Phe109fs|357/1003|326/927|109/308||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022150.1|protein_coding|2/14|c.326_327delTT|p.Phe109fs|357/1523|326/1437|109/478||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022151.1|protein_coding|2/13|c.326_327delTT|p.Phe109fs|357/1879|326/1431|109/476||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022157.1|protein_coding|2/10|c.326_327delTT|p.Phe109fs|357/1619|326/1131|109/376||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022153.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|356/1791|326/1344|109/447||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022155.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|355/3392|326/1257|109/418||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022152.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|354/4441|326/1368|109/455||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022154.1|protein_coding|2/12|c.269_270delTT|p.Phe90fs|495/4582|269/1311|90/436||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_001159508.1|protein_coding|1/10|c.154-131_154-130delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_002225.3|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_429453.3|pseudogene|2/12|n.344+83_344+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_017022156.1|protein_coding|2/11|c.186+83_186+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751264.1|pseudogene|2/10|n.634+83_634+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_005254350.2|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720492.2|protein_coding|2/12|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720495.2|protein_coding|2/9|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751263.1|pseudogene|2/12|n.593+83_593+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751262.1|pseudogene|2/13|n.593+83_593+84delTT||||||,GTT|non_coding_transcript_exon_variant|MODIFIER|IVD|IVD|transcript|XR_001751260.1|pseudogene|2/13|n.354_355delTT||||||;DP4=2,4,4,2;DP=14;FQ=57.4735;IDV=3;IMF=0.428571;INDEL;LOF=(IVD|IVD|20|0.45);MQ0F=0;MQ=60;MQSB=0.861511;PV4=1,0.0076542,1,0.150772;SF=0,1;SGB=-0.511536;VDB=0.520678	GT:DP:PL	0/1:6:92,0,124	0/1:6:92,0,124
chr15	40407805	.	GTTTT	GAA	54.47	.	AC1=1;AC=2;AF1=0.5;AN=4;ANN=GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022149.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|358/1798|326/1551|109/516||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022158.1|protein_coding|2/8|c.326_327delTT|p.Phe109fs|357/1003|326/927|109/308||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022150.1|protein_coding|2/14|c.326_327delTT|p.Phe109fs|357/1523|326/1437|109/478||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022151.1|protein_coding|2/13|c.326_327delTT|p.Phe109fs|357/1879|326/1431|109/476||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022157.1|protein_coding|2/10|c.326_327delTT|p.Phe109fs|357/1619|326/1131|109/376||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022153.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|356/1791|326/1344|109/447||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022155.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|355/3392|326/1257|109/418||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022152.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|354/4441|326/1368|109/455||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022154.1|protein_coding|2/12|c.269_270delTT|p.Phe90fs|495/4582|269/1311|90/436||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_001159508.1|protein_coding|1/10|c.154-131_154-130delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_002225.3|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_429453.3|pseudogene|2/12|n.344+83_344+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_017022156.1|protein_coding|2/11|c.186+83_186+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751264.1|pseudogene|2/10|n.634+83_634+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_005254350.2|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720492.2|protein_coding|2/12|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720495.2|protein_coding|2/9|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751263.1|pseudogene|2/12|n.593+83_593+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751262.1|pseudogene|2/13|n.593+83_593+84delTT||||||,GTT|non_coding_transcript_exon_variant|MODIFIER|IVD|IVD|transcript|XR_001751260.1|pseudogene|2/13|n.354_355delTT||||||;DP4=2,4,4,2;DP=14;FQ=57.4735;IDV=3;IMF=0.428571;INDEL;LOF=(IVD|IVD|20|0.45);MQ0F=0;MQ=60;MQSB=0.861511;PV4=1,0.0076542,1,0.150772;SF=0,1;SGB=-0.511536;VDB=0.520678	GT:DP:PL	0/1:6:92,0,124	0/1:6:92,0,124
chr15	40407805	.	GTTTT	AAA	54.47	.	AC1=1;AC=2;AF1=0.5;AN=4;ANN=GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022149.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|358/1798|326/1551|109/516||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022158.1|protein_coding|2/8|c.326_327delTT|p.Phe109fs|357/1003|326/927|109/308||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022150.1|protein_coding|2/14|c.326_327delTT|p.Phe109fs|357/1523|326/1437|109/478||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022151.1|protein_coding|2/13|c.326_327delTT|p.Phe109fs|357/1879|326/1431|109/476||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022157.1|protein_coding|2/10|c.326_327delTT|p.Phe109fs|357/1619|326/1131|109/376||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022153.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|356/1791|326/1344|109/447||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022155.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|355/3392|326/1257|109/418||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022152.1|protein_coding|2/12|c.326_327delTT|p.Phe109fs|354/4441|326/1368|109/455||,GTT|frameshift_variant|HIGH|IVD|IVD|transcript|XM_017022154.1|protein_coding|2/12|c.269_270delTT|p.Phe90fs|495/4582|269/1311|90/436||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_001159508.1|protein_coding|1/10|c.154-131_154-130delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|NM_002225.3|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_429453.3|pseudogene|2/12|n.344+83_344+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_017022156.1|protein_coding|2/11|c.186+83_186+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751264.1|pseudogene|2/10|n.634+83_634+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_005254350.2|protein_coding|2/11|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720492.2|protein_coding|2/12|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XM_006720495.2|protein_coding|2/9|c.243+83_243+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751263.1|pseudogene|2/12|n.593+83_593+84delTT||||||,GTT|intron_variant|MODIFIER|IVD|IVD|transcript|XR_001751262.1|pseudogene|2/13|n.593+83_593+84delTT||||||,GTT|non_coding_transcript_exon_variant|MODIFIER|IVD|IVD|transcript|XR_001751260.1|pseudogene|2/13|n.354_355delTT||||||;DP4=2,4,4,2;DP=14;FQ=57.4735;IDV=3;IMF=0.428571;INDEL;LOF=(IVD|IVD|20|0.45);MQ0F=0;MQ=60;MQSB=0.861511;PV4=1,0.0076542,1,0.150772;SF=0,1;SGB=-0.511536;VDB=0.520678	GT:DP:PL	0/1:6:92,0,124	0/1:6:92,0,124
chr21	28931066	rs58579273	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGTGTGTGTGTGT	123.48	.	AC1=1;AC=2,0,0;AF1=0.501256;AN=4;ANN=GGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_015565.2|protein_coding|29/29|c.5376+55_5376+60delACACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_015565.2|protein_coding|29/29|c.5376+55_5376+58delACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_015565.2|protein_coding|29/29|c.5376+54_5376+55insAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028317.1|protein_coding|19/19|c.3105+55_3105+60delACACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028317.1|protein_coding|19/19|c.3105+55_3105+58delACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028317.1|protein_coding|19/19|c.3105+54_3105+55insAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028316.1|protein_coding|28/28|c.4371+55_4371+60delACACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028316.1|protein_coding|28/28|c.4371+55_4371+58delACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|XM_017028316.1|protein_coding|28/28|c.4371+54_4371+55insAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_001320766.1|protein_coding|28/28|c.5334+55_5334+60delACACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_001320766.1|protein_coding|28/28|c.5334+55_5334+58delACAC||||||,GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT|intron_variant|MODIFIER|LTN1|LTN1|transcript|NM_001320766.1|protein_coding|28/28|c.5334+54_5334+55insAC||||||;ASP;DP4=2,0,16,0;DP=22;FQ=-11.8201;GENEINFO=LTN1:26046;IDV=9;IMF=0.818182;INDEL;INT;MQ0F=0;MQ=60;PV4=1,1,1,0.246313;RS=58579273;RSPOS=28931100;SAO=0;SF=0,1;SGB=-0.651104;SSR=0;VC=DIV;VDB=0.00542535;VP=0x050000080005000002000200;WGT=1;dbSNPBuildID=129	GT:DP:PL	0/1:9:246,85,108,138,0,163,198,66,119,227	0/1:9:246,85,108,138,0,163,198,66,119,227
