Mercurial > repos > iuc > gatk4_mutect2

annotate test-data/Mutect2-out1.vcf @ 0:f41a1e03538b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
author iuc
date Wed, 30 Oct 2019 15:33:59 -0400
parents
children fd2d6e035c3f
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f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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1 ##fileformat=VCFv4.2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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2 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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3 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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5 ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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6 ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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11 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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12 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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13 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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14 ##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.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 --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 --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 --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 --force-active false --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="4.1.4.0",Date="October 29, 2019 1:13:39 PM EDT">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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15 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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16 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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17 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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18 ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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19 ##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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20 ##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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21 ##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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22 ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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23 ##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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24 ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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25 ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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26 ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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27 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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28 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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29 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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30 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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31 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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32 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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33 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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34 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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35 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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36 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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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">
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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38 ##MutectVersion=2.2
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39 ##contig=<ID=K03455,length=9719>
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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40 ##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives.
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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41 ##source=Mutect2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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42 ##tumor_sample=SRR8525881
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43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
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44 K03455 4098 . T C . . DP=1;ECNT=12;MBQ=0,34;MFRL=0,158;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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45 K03455 4145 . T C . . DP=4;ECNT=12;MBQ=0,27;MFRL=0,242;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=17.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.800:4:0,1:0,3:0,0,3,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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46 K03455 4190 . A G . . DP=14;ECNT=12;MBQ=38,38;MFRL=290,278;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=50.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,12:0.786:14:0,4:1,8:0|1:4190_A_G:4190:2,0,10,2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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47 K03455 4209 . GC AC,AA . . DP=18;ECNT=12;MBQ=37,35,35;MFRL=200,295,290;MMQ=60,60,60;MPOS=10,43;POPAF=7.30,7.30;TLOD=13.72,52.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:1,4,13:0.263,0.632:18:1,2,4:0,2,9:1,0,15,2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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48 K03455 4233 . T C . . DP=24;ECNT=12;MBQ=38,39;MFRL=252,263;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=16.13 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:19,5:0.261:24:7,2:11,3:1|0:4190_A_G:4190:16,3,5,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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49 K03455 4250 . G A . . DP=36;ECNT=12;MBQ=37,37;MFRL=273,201;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=4.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,2:0.088:35:15,2:16,0:29,4,2,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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50 K03455 4259 . T A . . DP=40;ECNT=12;MBQ=35,35;MFRL=254,276;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=134.66 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,32:0.784:39:3,15:4,13:0|1:4259_T_A:4259:7,0,27,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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51 K03455 4262 . A T . . DP=40;ECNT=12;MBQ=37,37;MFRL=276,254;MMQ=60,60;MPOS=48;POPAF=7.30;TLOD=23.11 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:32,7:0.216:39:16,3:13,4:1|0:4259_T_A:4259:27,5,7,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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52 K03455 4268 . G A . . DP=40;ECNT=12;MBQ=34,37;MFRL=252,273;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=47.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:27,13:0.368:40:11,7:13,5:22,5,13,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
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53 K03455 4271 . A G . . DP=43;ECNT=12;MBQ=37,33;MFRL=250,287;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=28.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,9:0.244:43:14,7:15,2:29,5,9,0
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
54 K03455 4277 . C T . . DP=46;ECNT=12;MBQ=37,37;MFRL=244,276;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=148.83 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,36:0.767:46:3,18:4,16:0|1:4259_T_A:4259:9,1,31,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
55 K03455 4279 . GT AC,AT . . DP=47;ECNT=12;MBQ=37,35,36;MFRL=263,252,202;MMQ=60,60,60;MPOS=34,33;POPAF=7.30,7.30;TLOD=60.64,24.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:17,21,9:0.421,0.201:47:8,8,5:7,9,4:16,1,25,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
56 K03455 4310 . C T . . DP=39;ECNT=15;MBQ=20,18;MFRL=229,290;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=7.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,4:0.141:38:18,0:12,2:21,13,1,3
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
57 K03455 4313 . G A . . DP=37;ECNT=15;MBQ=20,32;MFRL=229,273;MMQ=60,60;MPOS=69;POPAF=7.30;TLOD=12.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,5:0.143:37:12,3:12,1:17,15,4,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
58 K03455 4320 . G A . . DP=38;ECNT=15;MBQ=20,20;MFRL=252,263;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=26.00 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,7:0.237:38:16,1:12,3:17,14,3,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
59 K03455 4330 . A G . . DP=42;ECNT=15;MBQ=20,38;MFRL=252,276;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=13.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,4:0.125:41:16,3:17,0:19,18,3,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
60 K03455 4334 . A G . . DP=43;ECNT=15;MBQ=32,36;MFRL=263,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=14.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,5:0.150:43:17,2:18,3:21,17,1,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
61 K03455 4340 . A G . . DP=45;ECNT=15;MBQ=37,20;MFRL=263,252;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=109.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,28:0.586:45:8,13:9,11:0|1:4340_A_G:4340:9,8,13,15
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
62 K03455 4343 . C A . . DP=43;ECNT=15;MBQ=33,20;MFRL=263,229;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=109.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,26:0.586:43:7,12:6,10:0|1:4340_A_G:4340:9,8,11,15
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
63 K03455 4345 . GC AT . . DP=47;ECNT=15;MBQ=20,37;MFRL=204,254;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=44.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,13:0.302:47:12,4:14,6:16,18,6,7
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
64 K03455 4346 . C T . . DP=46;ECNT=15;MBQ=20,26;MFRL=197,276;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=13.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,4:0.146:35:11,2:10,0:14,17,3,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
65 K03455 4358 . T C . . DP=45;ECNT=15;MBQ=20,35;MFRL=206,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,7:0.171:44:13,4:19,3:16,21,2,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
66 K03455 4361 . GCT ACT,G . . DP=47;ECNT=15;MBQ=36,20,35;MFRL=237,208,247;MMQ=60,60,60;MPOS=32,32;POPAF=7.30,7.30;TLOD=101.55,49.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:6,28,13:0.573,0.289:47:3,9,4:2,13,7:4,2,16,25
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
67 K03455 4364 . A AAG . . DP=49;ECNT=15;MBQ=33,35;MFRL=208,247;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=48.10 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,13:0.295:47:15,4:17,7:15,19,5,8
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
68 K03455 4370 . A G . . DP=51;ECNT=15;MBQ=20,37;MFRL=197,291;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=64.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:30,20:0.466:50:10,8:13,12:13,17,7,13
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
69 K03455 4376 . C T . . DP=53;ECNT=15;MBQ=29,25;MFRL=231,244;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=80.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,24:0.446:52:8,10:16,12:9,19,11,13
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
70 K03455 4397 . T C . . DP=57;ECNT=15;MBQ=34,37;MFRL=291,247;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=66.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,19:0.381:51:9,8:17,9:15,17,9,10
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
71 K03455 4416 . C T . . DP=65;ECNT=21;MBQ=37,37;MFRL=270,310;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=33.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:54,11:0.193:65:21,4:31,4:22,32,6,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
72 K03455 4418 . A G . . DP=64;ECNT=21;MBQ=37,37;MFRL=287,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:61,3:0.066:64:24,3:35,0:26,35,1,2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
73 K03455 4421 . T C . . DP=64;ECNT=21;MBQ=35,38;MFRL=259,291;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=140.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,36:0.574:64:15,13:10,21:11,17,16,20
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
74 K03455 4424 . T C . . DP=62;ECNT=21;MBQ=37,38;MFRL=251,291;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=104.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,29:0.498:61:14,9:12,17:12,20,14,15
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
75 K03455 4430 . T C . . DP=62;ECNT=21;MBQ=37,38;MFRL=284,265;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=3.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:60,2:0.051:62:24,2:31,0:25,35,1,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
76 K03455 4439 . A G . . DP=54;ECNT=21;MBQ=38,35;MFRL=291,241;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=18.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:48,6:0.115:54:21,2:24,4:21,27,2,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
77 K03455 4442 . AG GA . . DP=53;ECNT=21;MBQ=38,33;MFRL=290,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,7:0.159:52:18,2:23,5:19,26,3,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
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78 K03455 4443 . G A . . DP=53;ECNT=21;MBQ=37,38;MFRL=282,297;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=75.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:26,22:0.454:48:12,9:10,10:10,16,11,11
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
79 K03455 4448 . C A . . DP=51;ECNT=21;MBQ=38,20;MFRL=290,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=9.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:47,3:0.062:50:18,0:25,2:20,27,1,2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
80 K03455 4449 . C T . . DP=49;ECNT=21;MBQ=37,38;MFRL=209,323;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=90.60 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,24:0.511:49:11,10:13,13:11,14,11,13
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
81 K03455 4460 . T C . . DP=46;ECNT=21;MBQ=37,37;MFRL=284,329;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=18.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:40,6:0.159:46:15,2:22,3:20,20,2,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
82 K03455 4465 . T TGGCC . . DP=45;ECNT=21;MBQ=37,35;MFRL=310,176;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=26.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,8:0.170:43:12,6:21,1:17,18,4,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
83 K03455 4466 . A G,AGTG . . DP=44;ECNT=21;MBQ=38,38,37;MFRL=322,227,176;MMQ=60,60,60;MPOS=29,22;POPAF=7.30,7.30;TLOD=12.11,28.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:30,4,8:0.136,0.190:42:10,1,6:16,3,1:15,15,5,7
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
84 K03455 4478 . T C . . DP=33;ECNT=21;MBQ=37,33;MFRL=323,206;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=40.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:23,10:0.303:33:7,6:15,4:12,11,4,6
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
85 K03455 4505 . A G . . DP=19;ECNT=21;MBQ=39,38;MFRL=394,323;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=67.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,16:0.810:19:2,5:1,8:2,1,11,5
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
86 K03455 4508 . A T . . DP=17;ECNT=21;MBQ=39,35;MFRL=341,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,13:0.737:17:2,5:2,8:2,2,10,3
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
87 K03455 4511 . G A . . DP=17;ECNT=21;MBQ=37,36;MFRL=394,329;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=58.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,14:0.789:17:2,4:1,7:2,1,10,4
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
88 K03455 4526 . T C . . DP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,13:0.933:13:0,7:0,6:0,0,11,2
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
89 K03455 4528 . T TCA . . DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=5.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
90 K03455 4530 . CTT C . . DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1
f41a1e03538b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
iuc
parents:
diff changeset
91 K03455 4532 . T C . . DP=13;ECNT=21;MBQ=0,33;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,11:0.926:11:0,7:0,2:0,0,11,0