Mercurial > repos > iuc > gatk4_mutect2
diff test-data/Mutect2-out3.vcf @ 8:55e8a08e39e1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
| author | iuc |
|---|---|
| date | Tue, 03 Feb 2026 18:50:29 +0000 |
| parents | d2c0c2698f58 |
| children |
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--- a/test-data/Mutect2-out3.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out3.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##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"> @@ -11,19 +12,20 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##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"> +##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 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --base-qual-correction-factor 5 --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 --flow-mode NONE --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 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --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 --max-extension-into-assembly-region-padding-legacy 25 --enable-legacy-assembly-region-trimming 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 --max-variants-per-shard 0 --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="4.6.2.0",Date="February 2, 2026, 12:29:39?AM GMT"> ##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 |."> ##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"> ##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."> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -43,25 +45,23 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 +K03455 2644 . A G . . AS_SB_TABLE=41,9|2,0;BQHIST=20,18,0,32,1,0,37,12,0,38,4,1,39,15,1;DP=61;ECNT=6;ECNTH=6;MBQ=37,39;MFRL=242,292;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.99 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:50,2:0.064:52:21,0:21,2:42,2:41,9,2,0 +K03455 2652 . G A . . AS_SB_TABLE=0,0|122,15;BQHIST=16,1,0,18,9,0,20,27,0,29,5,0,32,21,0,33,13,0,34,2,0,37,27,0,38,16,0,39,14,0;DP=137;ECNT=6;ECNTH=5;MBQ=0,33;MFRL=0,266;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=614.56 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,137:0.992:137:0,53:0,59:0,124:0|1:2652_G_A:2652:0,0,122,15 +K03455 2660 . T C . . AS_SB_TABLE=0,0|152,18;BQHIST=15,1,0,16,1,0,17,3,0,20,27,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,50,0,38,27,0,39,22,0;DP=170;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,269;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=762.96 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,170:0.994:170:0,63:0,68:0,154:0|1:2652_G_A:2652:0,0,152,18 +K03455 2664 . A G . . AS_SB_TABLE=0,0|155,18;BQHIST=18,0,2,19,0,3,20,0,30,30,0,3,32,0,15,33,0,13,34,0,2,35,0,3,36,0,2,37,0,19,38,0,67,39,0,12;DP=173;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,267;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=774.91 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,173:0.994:173:0,76:0,76:0,157:0|1:2652_G_A:2652:0,0,155,18 +K03455 2669 . G A . . AS_SB_TABLE=0,0|162,20;BQHIST=16,2,0,18,1,0,19,2,0,20,35,0,29,1,0,32,5,0,33,9,0,34,3,0,36,1,0,37,47,0,38,44,0,39,32,0;DP=185;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,271;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=800.27 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,182:0.994:182:0,78:0,82:0,164:0|1:2652_G_A:2652:0,0,162,20 +K03455 2720 . T C . . AS_SB_TABLE=0,0|254,46;BQHIST=14,3,0,16,12,0,17,1,0,18,24,0,20,65,0,30,1,0,32,3,0,33,25,0,34,8,0,36,14,0,37,81,0,38,24,0,39,39,0;DP=348;ECNT=6;ECNTH=5;MBQ=0,36;MFRL=0,259;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1043.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,300:0.996:300:0,106:0,121:0,261:0,0,254,46 +K03455 2797 . G A . . AS_SB_TABLE=0,0|315,161;BQHIST=15,1,0,16,2,0,17,1,0,18,19,0,20,182,0,32,5,0,33,19,0,35,8,0,36,9,0,37,48,0,38,60,0,39,119,0;DP=504;ECNT=9;ECNTH=7;MBQ=0,35;MFRL=0,242;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=1635.75 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,476:0.998:476:0,185:0,168:0,395:0,0,315,161 +K03455 2831 . A T . . AS_SB_TABLE=315,204|0,18;BQHIST=14,0,4,15,0,13,16,1,2,17,3,50,18,11,14,19,0,3,20,0,148,29,0,3,30,1,5,31,0,6,32,0,8,33,2,42,34,0,15,36,0,6,37,0,53,38,0,45,39,0,100;DP=558;ECNT=9;ECNTH=8;MBQ=33,18;MFRL=238,273;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=4.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:519,18:0.024:537:182,0:156,0:432,12:315,204,0,18 +K03455 2848 . T TA . . AS_SB_TABLE=14,6|318,254;BQHIST=14,2,0,15,21,2,16,10,0,17,1,0,19,2,0,20,260,9,27,1,0,29,1,0,30,11,2,31,1,0,32,15,0,33,18,3,34,12,0,35,1,0,36,19,1,37,46,1,38,68,0,39,81,2;DP=621;ECNT=9;ECNTH=7;MBQ=20,20;MFRL=270,245;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1153.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,572:0.982:592:7,179:6,177:14,447:14,6,318,254 +K03455 2872 . T A . . AS_SB_TABLE=267,299|34,0;BQHIST=14,2,1,15,2,0,16,0,12,17,10,5,18,19,51,19,0,35,20,0,173,27,1,1,29,0,16,30,0,1,31,0,7,32,0,24,33,0,31,34,0,12,35,0,10,36,0,10,37,0,79,38,0,43,39,0,54;DP=639;ECNT=9;ECNTH=7;MBQ=29,18;MFRL=240,276;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:566,34:0.031:600:135,1:134,0:468,21:267,299,34,0 +K03455 2874 . C T . . AS_SB_TABLE=0,1|311,300;BQHIST=16,8,0,17,7,0,18,52,0,19,12,0,20,201,0,29,4,0,30,3,0,31,9,0,32,34,0,33,42,0,34,14,0,35,13,0,36,10,0,37,90,1,38,53,0,39,52,0;DP=615;ECNT=9;ECNTH=7;MBQ=37,32;MFRL=235,242;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=2682.59 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:1,611:0.996:612:1,174:0,160:1,505:0|1:2874_C_T:2874:0,1,311,300 +K03455 2882 . G T . . AS_SB_TABLE=4,2|290,266;BQHIST=14,1,0,16,5,1,17,3,2,18,22,0,19,11,0,20,200,0,29,1,1,30,4,0,31,4,1,32,5,0,33,24,0,34,1,0,35,19,0,36,9,0,37,87,0,38,53,0,39,106,0;DP=581;ECNT=9;ECNTH=7;MBQ=17,33;MFRL=276,247;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1871.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:6,556:0.994:562:1,167:0,157:4,457:4,2,290,266 +K03455 2894 . T C . . AS_SB_TABLE=0,0|294,271;BQHIST=14,1,0,15,6,0,16,4,0,17,13,0,18,32,0,19,4,0,20,167,0,27,1,0,29,2,0,30,2,0,31,2,0,32,9,0,33,27,0,34,10,0,35,6,0,36,8,0,37,81,0,38,65,0,39,116,0;DP=565;ECNT=9;ECNTH=7;MBQ=0,34;MFRL=0,250;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2595.31 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,565:0.998:565:0,146:0,153:0,476:0|1:2874_C_T:2874:0,0,294,271 +K03455 2906 . C T . . AS_SB_TABLE=0,0|249,259;BQHIST=16,2,0,18,4,0,19,10,0,20,155,0,30,1,0,31,2,0,32,4,0,33,18,0,34,3,0,35,17,0,36,10,0,37,62,0,38,79,0,39,141,0;DP=508;ECNT=9;ECNTH=7;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2422.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,508:0.998:508:0,132:0,159:0,440:0|1:2874_C_T:2874:0,0,249,259 +K03455 2913 . G A . . AS_SB_TABLE=0,0|248,257;BQHIST=17,1,0,18,5,0,19,5,0,20,140,0,29,1,0,30,2,0,31,1,0,32,2,0,33,15,0,34,1,0,35,4,0,36,3,0,37,62,0,38,71,0,39,180,0,40,4,0;DP=505;ECNT=9;ECNTH=7;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2413.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,505:0.998:505:0,133:0,157:0,438:0|1:2874_C_T:2874:0,0,248,257 +K03455 2987 . C T . . AS_SB_TABLE=0,0|76,130;BQHIST=16,4,0,17,4,0,19,5,0,20,15,0,30,1,0,31,6,0,32,8,0,33,30,0,34,8,0,35,9,0,36,1,0,37,46,0,38,31,0,39,38,0;DP=211;ECNT=5;ECNTH=3;MBQ=0,37;MFRL=0,270;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=782.35 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,206:0.995:206:0,85:0,96:0,199:0,0,76,130 +K03455 3016 . C A . . AS_SB_TABLE=57,28|6,0;BQHIST=14,0,2,15,0,1,18,5,24,20,0,5,29,0,1,30,0,2,32,0,4,33,1,10,34,0,2,35,0,2,36,0,8,37,0,5,38,0,15,39,0,4;DP=95;ECNT=5;ECNTH=3;MBQ=33,18;MFRL=278,272;MMQ=60,60;MPOS=6;POPAF=7.30;TLOD=4.56 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:85,6:0.073:91:23,1:31,0:83,6:57,28,6,0 +K03455 3020 . A G . . AS_SB_TABLE=0,0|59,26;BQHIST=14,0,12,16,0,1,18,0,1,20,0,4,27,0,2,29,0,1,30,0,7,32,0,8,33,0,2,34,0,1,36,0,19,37,0,4,38,0,22,39,0,1;DP=91;ECNT=5;ECNTH=3;MBQ=0,36;MFRL=0,289;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=292.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,85:0.988:85:0,30:0,37:0,83:0,0,59,26 +K03455 3036 . A G . . AS_SB_TABLE=16,3|3,0;BQHIST=15,1,0,19,7,2,29,1,0,30,1,0,33,3,0,37,4,1,38,2,0;DP=36;ECNT=5;ECNTH=4;MBQ=30,19;MFRL=289,298;MMQ=60,60;MPOS=0;POPAF=7.30;TLOD=4.59 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,3:0.160:22:7,1:3,0:19,3:0|1:3036_A_G:3036:16,3,3,0 +K03455 3038 . C G . . AS_SB_TABLE=16,3|3,0;BQHIST=14,0,1,19,5,0,30,1,0,32,1,0,33,1,0,35,1,0,37,1,0,38,2,0,39,3,0;DP=22;ECNT=5;ECNTH=4;MBQ=33,14;MFRL=289,298;MMQ=60,60;MPOS=8;POPAF=7.30;TLOD=4.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,3:0.166:22:5,0:4,0:19,3:0|1:3036_A_G:3036:16,3,3,0