Mercurial > repos > iuc > gatk4_mutect2

comparison test-data/Mutect2-out3.vcf @ 3:287c4af133e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80"
author iuc
date Sun, 10 May 2020 17:58:00 -0400
parents fd2d6e035c3f
children
comparison
equal deleted inserted replaced
2:3be27a9a7313 3:287c4af133e6
4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
5 ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> 5 ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
6 ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> 6 ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
9 ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> 9 ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
10 ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> 10 ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
11 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 11 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
12 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> 12 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
13 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> 13 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:25:49 PM EST"> 14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input tumor.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:32:12 PM CEST">
15 ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
16 ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
15 ##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20."> 17 ##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20.">
16 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> 18 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
17 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 19 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
18 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> 20 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
19 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> 21 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
26 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> 28 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
27 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> 29 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
28 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> 30 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
29 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> 31 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
30 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> 32 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
31 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> 33 ##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
32 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> 34 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
33 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> 35 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
34 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> 36 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
35 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> 37 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
36 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> 38 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
37 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> 39 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
38 ##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site">
39 ##MutectVersion=2.2 40 ##MutectVersion=2.2
40 ##contig=<ID=K03455,length=9719> 41 ##contig=<ID=K03455,length=9719>
41 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. 42 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.
42 ##source=Mutect2 43 ##source=Mutect2
43 ##tumor_sample=SRR8525881 44 ##tumor_sample=SRR8525881
44 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 45 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
45 K03455 2652 . G A . . BQHIST=16,1,0,18,9,0,20,25,0,29,5,0,32,20,0,33,12,0,34,2,0,37,27,0,38,13,0,39,13,0;DP=129;ECNT=6;MBQ=0,33;MFRL=0,273;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=571.21 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,129:0.992:129:0,57:0,60:0|1:2652_G_A:2652:0,0,115,14 46 K03455 2652 . G A . . AS_SB_TABLE=0,0|119,14;BQHIST=16,1,0,18,9,0,20,26,0,29,5,0,32,20,0,33,12,0,34,2,0,37,28,0,38,14,0,39,14,0;DP=133;ECNT=6;MBQ=0,33;MFRL=0,271;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=588.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,133:0.992:133:0,59:0,62:0|1:2652_G_A:2652:0,0,119,14
46 K03455 2660 . T C . . BQHIST=15,1,0,16,1,0,17,2,0,20,24,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,48,0,38,27,0,39,20,0;DP=162;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=717.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,162:0.993:162:0,66:0,69:0|1:2652_G_A:2652:0,0,145,17 47 K03455 2660 . T C . . AS_SB_TABLE=0,0|149,17;BQHIST=15,1,0,16,1,0,17,2,0,20,25,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,48,0,38,28,0,39,22,0;DP=166;ECNT=6;MBQ=0,37;MFRL=0,272;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=734.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,166:0.994:166:0,68:0,71:0|1:2652_G_A:2652:0,0,149,17
47 K03455 2664 . A G . . BQHIST=18,0,2,19,0,2,20,0,27,30,0,3,32,0,15,33,0,13,34,0,1,35,0,4,36,0,1,37,0,17,38,0,65,39,0,13;DP=165;ECNT=6;MBQ=0,37;MFRL=0,273;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=572.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,165:0.993:165:0,80:0,79:0,0,148,17 48 K03455 2664 . A G . . AS_SB_TABLE=0,0|152,17;BQHIST=18,0,2,19,0,2,20,0,28,30,0,3,32,0,15,33,0,13,34,0,1,35,0,4,36,0,2,37,0,18,38,0,65,39,0,14;DP=169;ECNT=6;MBQ=0,37;MFRL=0,271;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=586.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,169:0.994:169:0,82:0,81:0,0,152,17
48 K03455 2669 . G A . . BQHIST=16,1,0,18,1,0,19,2,0,20,32,0,29,1,0,32,5,0,33,8,0,34,3,0,36,1,0,37,45,0,38,44,0,39,31,0;DP=177;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=755.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,174:0.994:174:0,84:0,86:0|1:2652_G_A:2652:0,0,155,19 49 K03455 2669 . G A . . AS_SB_TABLE=0,0|159,19;BQHIST=16,1,0,18,1,0,19,2,0,20,33,0,29,1,0,32,5,0,33,9,0,34,3,0,36,1,0,37,46,0,38,45,0,39,31,0;DP=181;ECNT=6;MBQ=0,37;MFRL=0,272;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=772.57 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,178:0.994:178:0,86:0,88:0|1:2652_G_A:2652:0,0,159,19
49 K03455 2677 . A G . . BQHIST=15,3,0,17,1,0,18,1,0,19,4,0,20,35,2,33,6,0,34,9,0,36,2,0,37,29,0,38,36,0,39,55,2;DP=186;ECNT=6;MBQ=38,30;MFRL=273,240;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:181,4:0.024:185:83,2:89,2:162,19,3,1 50 K03455 2677 . A G . . AS_SB_TABLE=166,19|3,1;BQHIST=15,3,0,17,1,0,18,1,0,19,4,0,20,36,2,33,6,0,34,9,0,36,3,0,37,29,0,38,36,0,39,57,2;DP=190;ECNT=6;MBQ=38,30;MFRL=271,240;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:185,4:0.023:189:85,2:91,2:166,19,3,1
50 K03455 2720 . T C . . BQHIST=14,3,0,16,10,0,17,1,0,18,20,0,20,65,0,30,1,0,32,2,0,33,25,0,34,9,0,36,12,0,37,81,0,38,24,0,39,40,0;DP=339;ECNT=6;MBQ=0,36;MFRL=0,263;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1040.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,295:0.996:295:0,120:0,139:0,0,250,45 51 K03455 2720 . T C . . AS_SB_TABLE=0,0|255,45;BQHIST=14,3,0,16,11,0,17,1,0,18,21,0,20,65,0,30,1,0,32,2,0,33,25,0,34,9,0,36,13,0,37,82,0,38,24,0,39,41,0;DP=345;ECNT=6;MBQ=0,36;MFRL=0,262;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1056.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,300:0.996:300:0,120:0,142:0,0,255,45
51 K03455 2797 . G A . . BQHIST=15,2,0,16,3,0,17,1,0,18,22,0,20,188,0,32,5,0,33,21,0,35,8,0,36,8,0,37,56,0,38,62,0,39,110,0;DP=521;ECNT=12;MBQ=0,35;MFRL=0,246;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=1710.50 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,497:0.998:497:0,245:0,213:0,0,334,163 52 K03455 2797 . G A . . AS_SB_TABLE=0,0|328,159;BQHIST=15,2,0,16,2,0,17,1,0,18,21,0,20,184,0,32,5,0,33,20,0,35,7,0,36,8,0,37,55,0,38,61,0,39,109,0;DP=509;ECNT=12;MBQ=0,35;MFRL=0,247;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=1690.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,487:0.998:487:0,240:0,209:0,0,328,159
52 K03455 2831 . A T . . BQHIST=14,5,0,15,12,0,16,2,1,17,48,3,18,12,10,19,3,0,20,138,0,29,2,0,30,5,1,31,6,0,32,9,0,33,40,2,34,14,0,35,1,0,36,6,0,37,52,0,38,43,0,39,102,0;DP=534;ECNT=12;MBQ=33,18;MFRL=240,262;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=4.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:502,17:0.023:519:221,1:197,2:298,204,0,17 53 K03455 2831 . A T . . AS_SB_TABLE=297,202|0,17;BQHIST=14,5,0,15,11,0,16,2,1,17,47,3,18,12,10,19,3,0,20,137,0,29,2,0,30,5,1,31,6,0,32,10,0,33,40,2,34,14,0,36,5,0,37,52,0,38,43,0,39,102,0;DP=532;ECNT=12;MBQ=33,18;MFRL=240,262;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=4.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:499,17:0.024:516:221,1:195,2:297,202,0,17
53 K03455 2848 . T TA . . BQHIST=14,0,2,15,0,18,16,0,11,17,0,1,20,6,241,27,0,1,29,0,1,30,1,14,31,0,1,32,0,13,33,2,22,34,0,11,35,0,1,36,0,20,37,0,47,38,1,71,39,3,81;DP=596;ECNT=12;MBQ=30,30;MFRL=257,246;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1256.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,560:0.982:573:6,264:7,260:8,5,299,261 54 K03455 2848 . T TA . . AS_SB_TABLE=8,5|304,260;BQHIST=14,0,2,15,0,18,16,0,11,17,0,1,19,0,1,20,6,239,27,0,1,29,0,1,30,1,14,31,0,1,32,0,14,33,2,24,34,0,12,35,0,1,36,0,20,37,0,48,38,1,71,39,3,81;DP=599;ECNT=12;MBQ=30,30;MFRL=257,246;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1270.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,564:0.983:577:6,264:7,263:8,5,304,260
54 K03455 2849 . A AG . . BQHIST=14,0,8,15,0,1,16,0,2,17,0,1,18,0,16,19,1,0,20,2,269,27,0,1,29,0,2,30,1,8,31,0,2,32,0,4,33,0,17,34,1,6,35,0,4,36,0,33,37,1,38,38,0,100,39,2,62;DP=594;ECNT=12;MBQ=20,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:577,8:0.012:585:285,2:261,5:309,268,4,4 55 K03455 2849 . A AG . . AS_SB_TABLE=314,267|4,4;BQHIST=14,0,7,15,0,1,16,0,3,17,0,1,18,0,16,19,1,0,20,2,269,27,0,1,29,0,2,30,1,8,31,0,2,32,0,4,33,0,18,34,1,6,35,0,4,36,0,33,37,1,40,38,0,101,39,2,62;DP=597;ECNT=12;MBQ=20,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:581,8:0.012:589:285,2:265,5:314,267,4,4
55 K03455 2872 . T A . . BQHIST=14,1,2,15,2,0,16,0,10,17,6,6,18,15,51,19,0,38,20,0,164,27,1,1,29,0,16,30,0,3,31,0,9,32,0,20,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,46,39,0,53;DP=620;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:559,25:0.023:584:222,1:230,0:259,300,25,0 56 K03455 2872 . T A . . AS_SB_TABLE=267,300|25,0;BQHIST=14,1,2,15,2,0,16,0,11,17,6,6,18,15,51,19,0,38,20,0,167,27,1,1,29,0,16,30,0,3,31,0,9,32,0,22,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,48,39,0,53;DP=628;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:567,25:0.023:592:225,1:234,0:267,300,25,0
56 K03455 2874 . C T . . BQHIST=16,0,6,17,1,5,18,0,53,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,31,33,0,40,34,0,13,35,0,12,36,0,11,37,0,85,38,0,53,39,0,50;DP=598;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=2009.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,595:0.997:596:0,262:0,249:1,0,292,303 57 K03455 2874 . C T . . AS_SB_TABLE=1,0|300,303;BQHIST=16,0,6,17,1,5,18,0,54,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,32,33,0,41,34,0,13,35,0,13,36,0,11,37,0,87,38,0,54,39,0,51;DP=606;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=2043.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,603:0.997:604:0,265:0,253:1,0,300,303
57 K03455 2882 . G T . . BQHIST=14,1,0,16,5,0,17,7,0,18,21,0,19,12,0,20,194,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,19,0,36,11,0,37,82,0,38,50,0,39,111,0;DP=569;ECNT=12;MBQ=31,33;MFRL=360,246;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=1892.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,568:0.997:569:1,254:0,252:1,0,287,281 58 K03455 2882 . G T . . AS_SB_TABLE=1,0|295,283;BQHIST=14,2,0,16,6,0,17,6,0,18,21,0,19,12,0,20,195,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,21,0,36,11,0,37,85,0,38,52,0,39,112,0;DP=579;ECNT=12;MBQ=31,35;MFRL=360,246;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1927.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,578:0.997:579:1,259:0,256:1,0,295,283
58 K03455 2889 . G A . . BQHIST=14,0,11,15,0,1,16,0,4,17,0,4,18,0,13,19,0,17,20,0,189,29,0,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,14,37,1,76,38,1,70,39,2,94,40,0,1;DP=568;ECNT=12;MBQ=33,37;MFRL=249,308;MMQ=60,60;MPOS=53;POPAF=7.30;TLOD=8.92 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:552,7:0.016:559:244,4:256,3:282,270,6,1 59 K03455 2889 . G A . . AS_SB_TABLE=289,272|7,1;BQHIST=14,0,11,15,0,1,16,0,4,17,0,5,18,0,13,19,0,17,20,0,190,29,1,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,15,37,1,79,38,1,72,39,2,95,40,0,1;DP=580;ECNT=12;MBQ=33,36;MFRL=249,291;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:561,8:0.018:569:248,4:260,4:289,272,7,1
59 K03455 2891 . A G . . BQHIST=14,0,1,16,4,0,17,9,0,18,18,0,19,8,0,20,176,6,30,1,0,31,4,0,32,7,0,33,25,1,34,2,0,35,26,0,36,7,1,37,75,0,38,84,0,39,87,0;DP=564;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:543,9:0.013:552:237,4:257,4:276,267,5,4 60 K03455 2891 . A G . . AS_SB_TABLE=286,269|5,4;BQHIST=14,0,1,16,6,0,17,9,0,18,18,0,19,8,0,20,179,6,30,1,0,31,4,0,32,8,0,33,25,1,34,2,0,35,26,0,36,7,1,37,78,0,38,85,0,39,89,0;DP=576;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:555,9:0.013:564:243,4:261,4:286,269,5,4
60 K03455 2894 . T C . . BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,32,0,19,4,0,20,160,0,27,1,0,29,3,0,30,5,0,32,5,0,33,24,0,34,12,0,35,5,0,36,8,0,37,81,0,38,68,0,39,113,0;DP=551;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1769.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,551:0.998:551:0,236:0,249:0,0,280,271 61 K03455 2894 . T C . . AS_SB_TABLE=0,0|291,273;BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,33,0,19,4,0,20,162,0,27,1,0,29,3,0,30,5,0,31,1,0,32,6,0,33,25,0,34,12,0,35,5,0,36,8,0,37,83,0,38,69,0,39,116,0;DP=564;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1813.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,564:0.998:564:0,243:0,253:0,0,291,273
61 K03455 2906 . C T . . BQHIST=16,0,2,18,0,4,19,0,10,20,0,144,30,0,2,31,0,1,32,0,3,33,0,19,34,0,3,35,0,19,36,0,11,37,0,57,38,0,75,39,0,145;DP=495;ECNT=12;MBQ=0,37;MFRL=0,250;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2348.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,495:0.998:495:0,225:0,254:0|1:2906_C_T:2906:0,0,235,260 62 K03455 2906 . C T . . AS_SB_TABLE=0,0|246,262;BQHIST=16,0,2,18,0,4,19,0,10,20,0,145,30,0,2,31,0,2,32,0,3,33,0,21,34,0,3,35,0,19,36,0,11,37,0,61,38,0,79,39,0,146;DP=508;ECNT=12;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2411.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,508:0.998:508:0,232:0,260:0|1:2906_C_T:2906:0,0,246,262
62 K03455 2913 . G A . . BQHIST=18,4,0,19,5,0,20,132,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,4,0,36,1,0,37,62,0,38,65,0,39,182,0,40,4,0;DP=492;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2341.59 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,492:0.998:492:0,224:0,251:0|1:2906_C_T:2906:0,0,234,258 63 K03455 2913 . G A . . AS_SB_TABLE=0,0|245,260;BQHIST=18,5,0,19,5,0,20,134,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,6,0,36,2,0,37,64,0,38,68,0,39,184,0,40,4,0;DP=505;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2402.33 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,505:0.998:505:0,230:0,257:0|1:2906_C_T:2906:0,0,245,260
63 K03455 2987 . C T . . BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,219:0.995:219:0,99:0,103:0,0,86,133 64 K03455 2987 . C T . . AS_SB_TABLE=0,0|86,133;BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,219:0.995:219:0,99:0,103:0,0,86,133
64 K03455 2992 . T G . . BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.86 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:179,9:0.043:188:74,2:77,0:74,105,9,0 65 K03455 2992 . T G . . AS_SB_TABLE=74,105|9,0;BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:179,9:0.043:188:74,2:77,0:74,105,9,0
65 K03455 3016 . C A . . BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:88,7:0.081:95:24,1:34,0:61,27,7,0 66 K03455 3016 . C A . . AS_SB_TABLE=61,27|7,0;BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:88,7:0.081:95:24,1:34,0:61,27,7,0
66 K03455 3020 . A G . . BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,90:0.989:90:0,32:0,43:0,0,65,25 67 K03455 3020 . A G . . AS_SB_TABLE=0,0|65,25;BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,90:0.989:90:0,32:0,43:0,0,65,25