#=GENOME_DIFF 1.0 #=COMMAND breseq -j 8 -r /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk /data/pg-molgen/harma/2021_04/fastq/8A_S8_R1_001.fastq.gz -o /data/pg-molgen/harma/2021_04/results_breseq/HK7_r1t #=REFSEQ /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk #=READSEQ /data/pg-molgen/harma/2021_04/fastq/8A_S8_R1_001.fastq.gz #=CONVERTED-BASES 1334109450 #=CONVERTED-READS 17788126 #=INPUT-BASES 1334309625 #=INPUT-READS 17790795 #=MAPPED-BASES 19754054 #=MAPPED-READS 282289 INS 1 12 NC_004302 3547 A gene_name=r1tp05 gene_position=coding (307/798 nt) gene_product=ORF5 gene_strand=> genes_inactivated=r1tp05 locus_tag=r1tp05 locus_tags_inactivated=r1tp05 mutation_category=small_indel position_end=3547 position_start=3547 ref_seq=A INS 2 13,14 NC_004302 3556 GT gene_name=r1tp05 gene_position=coding (316/798 nt) gene_product=ORF5 gene_strand=> genes_inactivated=r1tp05 locus_tag=r1tp05 locus_tags_inactivated=r1tp05 mutation_category=small_indel position_end=3556 position_start=3556 ref_seq=T SUB 3 15,16 NC_004302 5234 2 GC gene_name=r1tp09 gene_position=coding (325-326/834 nt) gene_product=ORF9 gene_strand=> genes_inactivated=r1tp09 locus_tag=r1tp09 locus_tags_inactivated=r1tp09 mutation_category=small_indel position_end=5235 position_start=5234 ref_seq=CG SNP 4 17 NC_004302 5237 G aa_new_seq=V aa_position=110 aa_ref_seq=L codon_new_seq=GTT codon_number=110 codon_position=1 codon_ref_seq=CTT gene_name=r1tp09 gene_position=328 gene_product=ORF9 gene_strand=> genes_overlapping=r1tp09 locus_tag=r1tp09 locus_tags_overlapping=r1tp09 mutation_category=snp_nonsynonymous position_end=5237 position_start=5237 ref_seq=C snp_type=nonsynonymous transl_table=11 DEL 5 18,19,20,21,22,23 NC_004302 8712 6 gene_name=r1tp14 gene_position=coding (21-26/396 nt) gene_product=ORF14 gene_strand=> genes_inactivated=r1tp14 locus_tag=r1tp14 locus_tags_inactivated=r1tp14 mutation_category=small_indel position_end=8717 position_start=8712 ref_seq=TGAATT repeat_length=6 repeat_new_copies=2 repeat_ref_copies=3 repeat_seq=TGAATT SNP 6 24 NC_004302 9972 A aa_new_seq=E aa_position=59 aa_ref_seq=A codon_new_seq=GAA codon_number=59 codon_position=2 codon_ref_seq=GCA gene_name=r1tp18 gene_position=176 gene_product=ORF18 gene_strand=> genes_overlapping=r1tp18 locus_tag=r1tp18 locus_tags_overlapping=r1tp18 mutation_category=snp_nonsynonymous position_end=9972 position_start=9972 ref_seq=C snp_type=nonsynonymous transl_table=11 SNP 7 25 NC_004302 13763 C aa_new_seq=A aa_position=122 aa_ref_seq=V codon_new_seq=GCT codon_number=122 codon_position=2 codon_ref_seq=GTT gene_name=r1tp24 gene_position=365 gene_product=ORF24 gene_strand=> genes_overlapping=r1tp24 locus_tag=r1tp24 locus_tags_overlapping=r1tp24 mutation_category=snp_nonsynonymous position_end=13763 position_start=13763 ref_seq=T snp_type=nonsynonymous transl_table=11 SNP 8 27 NC_004302 23480 C aa_new_seq=A aa_position=213 aa_ref_seq=E codon_new_seq=GCA codon_number=213 codon_position=2 codon_ref_seq=GAA gene_name=r1tp40 gene_position=638 gene_product=ORF40 gene_strand=> genes_overlapping=r1tp40 locus_tag=r1tp40 locus_tags_overlapping=r1tp40 mutation_category=snp_nonsynonymous position_end=23480 position_start=23480 ref_seq=A snp_type=nonsynonymous transl_table=11 RA 9 . NC_004302 1914 0 T C bias_e_value=29534.9 bias_p_value=0.885604 consensus_reject=FREQUENCY_CUTOFF consensus_score=198.9 fisher_strand_p_value=0.573978 frequency=2.331e-01 gene_name=r1tp02/rro gene_position=intergenic (-54/+7) gene_product=ORF2/Repressor protein gene_strand= ks_quality_p_value=0.122456 locus_tag=r1tp03/r1tp04 major_base=C major_cov=16/0 major_frequency=5.333e-01 minor_base=G minor_cov=14/0 new_cov=14/0 polymorphism_frequency=4.667e-01 polymorphism_score=29.0 prediction=polymorphism ref_cov=16/0 snp_type=intergenic total_cov=40/0 RA 11 . NC_004302 2995 1 . A bias_e_value=32935 bias_p_value=0.987555 consensus_reject=FREQUENCY_CUTOFF consensus_score=302.4 fisher_strand_p_value=1 frequency=2.160e-01 gene_name=tec gene_position=coding (9/243 nt) gene_product=tec gene_strand=> ks_quality_p_value=0.846441 locus_tag=r1tp04 major_base=. major_cov=126/1 major_frequency=7.840e-01 minor_base=A minor_cov=35/0 new_cov=35/0 polymorphism_frequency=2.160e-01 polymorphism_score=69.6 prediction=polymorphism ref_cov=126/1 total_cov=161/1 RA 12 . NC_004302 3545 1 . A bias_e_value=33312 bias_p_value=0.998862 consensus_score=1096.9 fisher_strand_p_value=1 frequency=1 gene_name=r1tp05 gene_position=coding (305/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=0.952672 locus_tag=r1tp05 major_base=A major_cov=427/5 major_frequency=9.818e-01 minor_base=. minor_cov=8/0 new_cov=427/5 polymorphism_frequency=9.818e-01 polymorphism_score=5.6 prediction=consensus ref_cov=8/0 total_cov=435/5 RA 13 . NC_004302 3554 1 . G bias_e_value=33350 bias_p_value=1 consensus_score=1300.3 fisher_strand_p_value=1 frequency=1 gene_name=r1tp05 gene_position=coding (314/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=1 locus_tag=r1tp05 major_base=G major_cov=447/5 major_frequency=9.168e-01 minor_base=. minor_cov=41/0 new_cov=447/5 polymorphism_frequency=9.168e-01 polymorphism_score=67.8 prediction=consensus ref_cov=41/0 total_cov=489/5 RA 14 . NC_004302 3554 2 . T bias_e_value=33350 bias_p_value=1 consensus_score=1236.2 fisher_strand_p_value=1 frequency=1 gene_name=r1tp05 gene_position=coding (314/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=1 locus_tag=r1tp05 major_base=T major_cov=448/5 major_frequency=9.170e-01 minor_base=. minor_cov=41/0 new_cov=448/5 polymorphism_frequency=9.170e-01 polymorphism_score=72.1 prediction=consensus ref_cov=41/0 total_cov=489/5 RA 15 . NC_004302 5234 0 C G aa_new_seq=A aa_position=109 aa_ref_seq=R bias_e_value=33349.5 bias_p_value=0.999985 codon_new_seq=GCA codon_number=109 codon_position=1 codon_ref_seq=CGA consensus_score=64.5 fisher_strand_p_value=1 frequency=1 gene_name=r1tp09 gene_position=325 gene_product=ORF9 gene_strand=> ks_quality_p_value=0.994521 locus_tag=r1tp09 major_base=G major_cov=25/1 major_frequency=9.286e-01 minor_base=C minor_cov=2/0 new_cov=25/1 new_seq=G polymorphism_frequency=9.286e-01 polymorphism_score=-0.3 prediction=consensus ref_cov=2/0 ref_seq=C snp_type=nonsynonymous total_cov=27/1 transl_table=11 RA 16 . NC_004302 5235 0 G C aa_new_seq=A aa_position=109 aa_ref_seq=R bias_e_value=33350 bias_p_value=1 codon_new_seq=GCA codon_number=109 codon_position=2 codon_ref_seq=CGA consensus_score=66.7 fisher_strand_p_value=1 frequency=1 gene_name=r1tp09 gene_position=326 gene_product=ORF9 gene_strand=> ks_quality_p_value=1 locus_tag=r1tp09 major_base=C major_cov=25/1 major_frequency=9.286e-01 minor_base=A minor_cov=2/0 new_cov=25/1 new_seq=C polymorphism_frequency=9.286e-01 polymorphism_score=-0.9 prediction=consensus ref_cov=1/0 ref_seq=G snp_type=nonsynonymous total_cov=28/1 transl_table=11 RA 17 . NC_004302 5237 0 C G aa_new_seq=V aa_position=110 aa_ref_seq=L bias_e_value=33349.5 bias_p_value=0.999985 codon_new_seq=GTT codon_number=110 codon_position=1 codon_ref_seq=CTT consensus_score=64.4 fisher_strand_p_value=1 frequency=1 gene_name=r1tp09 gene_position=328 gene_product=ORF9 gene_strand=> ks_quality_p_value=0.994521 locus_tag=r1tp09 major_base=G major_cov=25/1 major_frequency=9.286e-01 minor_base=T minor_cov=2/0 new_cov=25/1 new_seq=G polymorphism_frequency=9.286e-01 polymorphism_score=-1.1 prediction=consensus ref_cov=1/0 ref_seq=C snp_type=nonsynonymous total_cov=28/1 transl_table=11 RA 18 . NC_004302 8696 0 A . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (159/165 nt)|coding (5/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 19 . NC_004302 8697 0 A . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (160/165 nt)|coding (6/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 20 . NC_004302 8698 0 T . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (161/165 nt)|coding (7/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 21 . NC_004302 8699 0 T . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (162/165 nt)|coding (8/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 22 . NC_004302 8700 0 T . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (163/165 nt)|coding (9/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 23 . NC_004302 8701 0 G . consensus_score=20.9 frequency=1 gene_name=r1tp13|r1tp14 gene_position=coding (164/165 nt)|coding (10/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> locus_tag=r1tp13|r1tp14 major_base=. major_cov=7/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/1 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 snp_type=| total_cov=7/1 RA 24 . NC_004302 9972 0 C A aa_new_seq=E aa_position=59 aa_ref_seq=A codon_new_seq=GAA codon_number=59 codon_position=2 codon_ref_seq=GCA consensus_score=92.3 frequency=1 gene_name=r1tp18 gene_position=176 gene_product=ORF18 gene_strand=> locus_tag=r1tp18 major_base=A major_cov=38/0 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=38/0 new_seq=A polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 ref_seq=C snp_type=nonsynonymous total_cov=38/0 transl_table=11 RA 25 . NC_004302 13763 0 T C aa_new_seq=A aa_position=122 aa_ref_seq=V bias_e_value=33345.9 bias_p_value=0.999876 codon_new_seq=GCT codon_number=122 codon_position=2 codon_ref_seq=GTT consensus_score=53.0 fisher_strand_p_value=1 frequency=1 gene_name=r1tp24 gene_position=365 gene_product=ORF24 gene_strand=> ks_quality_p_value=0.984314 locus_tag=r1tp24 major_base=C major_cov=19/3 major_frequency=9.565e-01 minor_base=T minor_cov=1/0 new_cov=19/3 new_seq=C polymorphism_frequency=9.565e-01 polymorphism_score=-2.6 prediction=consensus ref_cov=1/0 ref_seq=T snp_type=nonsynonymous total_cov=20/3 transl_table=11 RA 26 . NC_004302 15047 1 . A bias_e_value=26975.4 bias_p_value=0.808858 consensus_reject=FREQUENCY_CUTOFF consensus_score=485.9 fisher_strand_p_value=0.587123 frequency=2.103e-01 gene_name=r1tp26/r1tp27 gene_position=intergenic (+140/-7) gene_product=HNH endonuclease/Structural protein gene_strand=>/> ks_quality_p_value=0.765446 locus_tag=r1tp26/r1tp27 major_base=. major_cov=194/5 major_frequency=7.897e-01 minor_base=A minor_cov=53/0 new_cov=53/0 polymorphism_frequency=2.103e-01 polymorphism_score=106.2 prediction=polymorphism ref_cov=194/5 snp_type=intergenic total_cov=247/5 RA 27 . NC_004302 23480 0 A C aa_new_seq=A aa_position=213 aa_ref_seq=E bias_e_value=33347.5 bias_p_value=0.999924 codon_new_seq=GCA codon_number=213 codon_position=2 codon_ref_seq=GAA consensus_score=296.0 fisher_strand_p_value=1 frequency=1 gene_name=r1tp40 gene_position=638 gene_product=ORF40 gene_strand=> ks_quality_p_value=0.9877 locus_tag=r1tp40 major_base=C major_cov=110/0 major_frequency=9.244e-01 minor_base=A minor_cov=9/0 new_cov=110/0 new_seq=C polymorphism_frequency=9.244e-01 polymorphism_score=9.0 prediction=consensus ref_cov=9/0 ref_seq=A snp_type=nonsynonymous total_cov=120/0 transl_table=11 RA 28 . NC_004302 24164 1 . T bias_e_value=32086.8 bias_p_value=0.962122 consensus_reject=FREQUENCY_CUTOFF consensus_score=65.0 fisher_strand_p_value=1 frequency=3.671e-01 gene_name=r1tp41/r1tp42 gene_position=intergenic (+54/-165) gene_product=ORF41/ORF42 gene_strand=>/> ks_quality_p_value=0.737701 locus_tag=r1tp41/r1tp42 major_base=. major_cov=50/0 major_frequency=6.329e-01 minor_base=T minor_cov=29/0 new_cov=29/0 polymorphism_frequency=3.671e-01 polymorphism_score=72.2 prediction=polymorphism ref_cov=50/0 snp_type=intergenic total_cov=79/0 MC 29 . NC_004302 1 11 0 0 gene_name=–/r1tp01 gene_position=intergenic (–/+83) gene_product=–/Integrase gene_strand=–/< left_inside_cov=0 left_outside_cov=NA locus_tag=–/r1tp01 right_inside_cov=0 right_outside_cov=2 MC 30 . NC_004302 33195 33350 0 0 gene_name=[r1tp50] gene_product=[r1tp50] left_inside_cov=1 left_outside_cov=2 locus_tag=[r1tp50] right_inside_cov=0 right_outside_cov=NA JC 31 . NC_004302 23379 -1 NC_004302 24308 1 0 alignment_overlap=0 coverage_minus=32 coverage_plus=1 flanking_left=75 flanking_right=75 frequency=1 junction_possible_overlap_registers=74 key=NC_004302__23379__-1__NC_004302__24308__1__0____75__75__0__0 max_left=73 max_left_minus=73 max_left_plus=43 max_min_left=29 max_min_left_minus=29 max_min_left_plus=0 max_min_right=32 max_min_right_minus=31 max_min_right_plus=32 max_pos_hash_score=148 max_right=73 max_right_minus=73 max_right_plus=32 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=0.81 new_junction_read_count=475 polymorphism_frequency=9.143e-01 pos_hash_score=19 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.05 side_1_overlap=0 side_1_possible_overlap_registers=74 side_1_read_count=27 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.11 side_2_overlap=0 side_2_possible_overlap_registers=74 side_2_read_count=62 side_2_redundant=0 total_non_overlap_reads=33 JC 32 . NC_004302 32569 1 NC_004302 32599 1 0 alignment_overlap=5 coverage_minus=0 coverage_plus=10 flanking_left=75 flanking_right=75 frequency=1.000e-01 junction_possible_overlap_registers=69 key=NC_004302__32569__1__NC_004302__32594__1__5____75__75__0__0 max_left=68 max_left_minus=0 max_left_plus=68 max_min_left=0 max_min_left_minus=0 max_min_left_plus=0 max_min_right=20 max_min_right_minus=0 max_min_right_plus=20 max_pos_hash_score=138 max_right=20 max_right_minus=0 max_right_plus=20 neg_log10_pos_hash_p_value=0.4 new_junction_coverage=0.66 new_junction_read_count=359 polymorphism_frequency=1.000e-01 pos_hash_score=8 prediction=polymorphism reject=FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=6.74 side_1_overlap=5 side_1_possible_overlap_registers=74 side_1_read_count=3957 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=5.06 side_2_overlap=0 side_2_possible_overlap_registers=69 side_2_read_count=2770 side_2_redundant=0 total_non_overlap_reads=10 UN 33 . NC_004302 1 36 UN 34 . NC_004302 148 157 UN 35 . NC_004302 332 332 UN 36 . NC_004302 334 334 UN 37 . NC_004302 468 468 UN 38 . NC_004302 641 650 UN 39 . NC_004302 658 658 UN 40 . NC_004302 1034 1034 UN 41 . NC_004302 1217 1220 UN 42 . NC_004302 1225 1225 UN 43 . NC_004302 1253 1316 UN 44 . NC_004302 2843 2843 UN 45 . NC_004302 4782 4819 UN 46 . NC_004302 7255 7255 UN 47 . NC_004302 7258 7291 UN 48 . NC_004302 7714 7752 UN 49 . NC_004302 14523 14523 UN 50 . NC_004302 33030 33350