Mercurial > repos > iuc > gatk4_mutect2
comparison test-data/Mutect2-out4.vcf @ 3:287c4af133e6 draft
"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 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --minimum-allele-fraction 0.0 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --pruning-lod-threshold 2.30258509299 --max-unpruned-variants 100 --base-quality-score-threshold 18 --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-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 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 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --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 --independent-mates false --disable-adaptive-pruning 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 --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --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 --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --force-call-filtered-alleles false --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 4:26:31 PM EST"> | 14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --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 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --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 --base-quality-score-threshold 18 --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-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --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 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --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 --add-output-sam-program-record true --add-output-vcf-command-line true --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 --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --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 3:32:53 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=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> | 17 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> |
| 16 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | 18 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> |
| 17 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> | 19 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> |
| 18 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> | 20 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> |
| 19 ##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> | 21 ##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> |
| 25 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> | 27 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> |
| 26 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> | 28 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> |
| 27 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> | 29 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> |
| 28 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> | 30 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> |
| 29 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> | 31 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> |
| 30 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> | 32 ##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> |
| 31 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> | 33 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> |
| 32 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> | 34 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> |
| 33 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> | 35 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> |
| 34 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> | 36 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> |
| 35 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> | 37 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> |
| 36 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> | 38 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> |
| 37 ##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"> | |
| 38 ##MutectVersion=2.2 | 39 ##MutectVersion=2.2 |
| 39 ##contig=<ID=K03455,length=9719> | 40 ##contig=<ID=K03455,length=9719> |
| 40 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. | 41 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. |
| 41 ##source=Mutect2 | 42 ##source=Mutect2 |
| 42 ##tumor_sample=SRR8525881 | 43 ##tumor_sample=SRR8525881 |
| 43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 | 44 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 |
| 44 K03455 6822 . GT AC . . DP=2;ECNT=1;MBQ=0,29;MFRL=0,117;MMQ=60,60;MPOS=79;POPAF=7.30;TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.750:2:0,0:0,2:0,0,0,2 | 45 K03455 6822 . GT AC . . AS_SB_TABLE=0,0|2,2;DP=4;ECNT=1;MBQ=0,38;MFRL=0,117;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=7.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.750:4:0,0:0,4:0,0,2,2 |
| 45 K03455 6902 . A C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 46 K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 46 K03455 6905 . A G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 47 K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 47 K03455 6911 . T C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 48 K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 48 K03455 6917 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 49 K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 49 K03455 6920 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 50 K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 50 K03455 6923 . C T . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 51 K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 51 K03455 6931 . C A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 52 K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 52 K03455 6936 . C G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 | 53 K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 |
| 53 K03455 7441 . A ACCT . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 54 K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 |
| 54 K03455 7443 . A AGTG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 55 K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 |
| 55 K03455 7449 . G A . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 56 K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 |
| 56 K03455 7452 . GGA G . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=103;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 57 K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 |
| 57 K03455 7455 . A ATG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=106;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 58 K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 |
| 58 K03455 7457 . TGA T . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=108;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 59 K03455 7163 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,13;MFRL=0,310;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,0:0,0,0,1 |
| 59 K03455 7460 . CA C . . DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 | 60 K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 |
| 60 K03455 7468 . CC TA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=114;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 | 61 K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 |
| 61 K03455 7478 . C T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 | 62 K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 62 K03455 7491 . A T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=104;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 | 63 K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 63 K03455 7494 . A G . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 | 64 K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 64 K03455 7508 . GA AG . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=87;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 | 65 K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 65 K03455 7541 . C CGA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 66 K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 66 K03455 7542 . AGT A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=53;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 67 K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 67 K03455 7548 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=47;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 68 K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 |
| 68 K03455 7555 . GA AT . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=40;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 69 K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 |
| 69 K03455 7560 . TC GT . . DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=35;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 70 K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 |
| 70 K03455 7568 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=-1073741804;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 71 K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 |
| 71 K03455 7571 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=24;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 72 K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 |
| 72 K03455 7581 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=14;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 73 K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 |
| 73 K03455 7584 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=11;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 74 K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 |
| 74 K03455 7603 . A AGGG . . DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=-8;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | 75 K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 |
| 75 K03455 7604 . T G . . DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=-22;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2 | 76 K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 |
| 77 K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 78 K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 79 K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 80 K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 81 K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 82 K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 83 K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 | |
| 84 K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2 |