##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##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=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">
##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">
##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  --tumor-sample SRR8525881 --output output.vcf --interval-set-rule UNION --interval-exclusion-padding 0 --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 --read-filter AmbiguousBaseReadFilter --read-filter FirstOfPairReadFilter --read-filter GoodCigarReadFilter  --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-padding 0 --interval-merging-rule ALL --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-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --ambig-filter-frac 0.05 --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 1:14:20 PM EDT">
##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=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=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=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.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
##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">
##MutectVersion=2.2
##contig=<ID=K03455,length=9719>
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##source=Mutect2
##tumor_sample=SRR8525881
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
K03455	4861	.	A	G	.	.	DP=1;ECNT=14;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
K03455	4918	.	G	A	.	.	DP=7;ECNT=14;MBQ=38,37;MFRL=303,370;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=8.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:3,3:0.499:6:2,0:1,2:2,1,0,3
K03455	4923	.	A	G	.	.	DP=8;ECNT=14;MBQ=0,33;MFRL=0,314;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=34.22	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,8:0.900:8:0,3:0,3:0,0,3,5
K03455	4949	.	G	A	.	.	DP=12;ECNT=14;MBQ=38,37;MFRL=285,264;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=27.49	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:5,7:0.573:12:2,2:1,4:0|1:4949_G_A:4949:2,3,2,5
K03455	4952	.	C	T	.	.	DP=13;ECNT=14;MBQ=36,37;MFRL=285,264;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=27.48	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:5,7:0.573:12:1,2:2,5:0|1:4949_G_A:4949:2,3,2,5
K03455	4988	.	T	C	.	.	DP=22;ECNT=14;MBQ=36,38;MFRL=285,278;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=14.99	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:17,5:0.250:22:5,2:8,2:6,11,3,2
K03455	4991	.	T	C	.	.	DP=22;ECNT=14;MBQ=37,28;MFRL=271,309;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=4.85	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:20,2:0.125:22:8,0:10,1:9,11,0,2
K03455	4996	.	AC	GA	.	.	DP=25;ECNT=14;MBQ=38,32;MFRL=285,203;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.72	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:21,3:0.152:24:6,1:10,1:8,13,1,2
K03455	4997	.	C	T,A	.	.	DP=25;ECNT=14;MBQ=38,37,38;MFRL=282,292,264;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=8.86,34.99	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:8,3,13:0.148,0.517:24:4,0,5:3,2,8:5,3,5,11
K03455	5004	.	G	A	.	.	DP=26;ECNT=14;MBQ=37,36;MFRL=262,288;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=4.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:24,2:0.107:26:7,1:13,1:8,16,1,1
K03455	5015	.	A	G	.	.	DP=34;ECNT=14;MBQ=38,38;MFRL=269,258;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=88.69	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:10,22:0.677:32:4,5:6,16:4,6,5,17
K03455	5018	.	A	G	.	.	DP=34;ECNT=14;MBQ=38,38;MFRL=262,261;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=11.32	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:30,4:0.139:34:9,0:15,4:10,20,0,4
K03455	5027	.	G	A	.	.	DP=37;ECNT=14;MBQ=37,38;MFRL=260,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.64	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:31,5:0.157:36:10,0:18,5:0|1:5027_G_A:5027:10,21,0,5
K03455	5036	.	G	A	.	.	DP=36;ECNT=14;MBQ=39,38;MFRL=256,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.71	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:30,5:0.162:35:9,0:18,4:0|1:5027_G_A:5027:10,20,0,5
K03455	5076	.	A	G	.	.	DP=37;ECNT=27;MBQ=38,37;MFRL=278,190;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.35	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:31,5:0.158:36:5,0:25,5:0|1:5076_A_G:5076:5,26,0,5
K03455	5098	.	A	G	.	.	DP=42;ECNT=27;MBQ=38,38;MFRL=190,292;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=126.26	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:7,32:0.804:39:0,4:7,22:0,7,4,28
K03455	5099	.	C	T	.	.	DP=42;ECNT=27;MBQ=38,37;MFRL=292,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=22.52	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:34,7:0.186:41:4,0:28,6:0|1:5076_A_G:5076:4,30,0,7
K03455	5121	.	C	T	.	.	DP=41;ECNT=27;MBQ=37,38;MFRL=257,205;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=24.97	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:33,8:0.209:41:3,1:28,6:3,30,1,7
K03455	5130	.	TG	CA	.	.	DP=38;ECNT=27;MBQ=38,38;MFRL=194,275;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=122.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:8,30:0.778:38:0,0:7,28:0,8,2,28
K03455	5131	.	G	A	.	.	DP=38;ECNT=27;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=23.77	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,8:0.932:8:0,1:0,6:0,0,1,7
K03455	5133	.	T	C	.	.	DP=36;ECNT=27;MBQ=38,36;MFRL=293,216;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=31.26	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:27,9:0.268:36:2,0:23,8:0|1:5133_T_C:5133:2,25,0,9
K03455	5137	.	GG	AG,AA	.	.	DP=35;ECNT=27;MBQ=39,39,39;MFRL=194,216,337;MMQ=60,60,60;MPOS=34,28;POPAF=7.30,7.30;TLOD=31.44,66.06	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:8,9,18:0.270,0.495:35:0,0,1:7,8,16:0,8,1,26
K03455	5146	.	AGG	A	.	.	DP=33;ECNT=27;MBQ=38,38;MFRL=315,216;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=31.38	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:24,9:0.286:33:1,0:22,9:0|1:5133_T_C:5133:1,23,0,9
K03455	5147	.	G	A	.	.	DP=33;ECNT=27;MBQ=38,37;MFRL=181,343;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=66.04	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:7,17:0.694:24:0,0:6,13:0|1:5147_G_A:5147:0,7,1,16
K03455	5153	.	GGTTT	G	.	.	DP=29;ECNT=27;MBQ=38,38;MFRL=296,216;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.02	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:20,9:0.323:29:0,0:19,9:0|1:5133_T_C:5133:0,20,0,9
K03455	5155	.	T	C	.	.	DP=28;ECNT=27;MBQ=38,38;MFRL=169,331;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=49.64	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:6,13:0.669:19:0,0:6,12:0|1:5147_G_A:5147:0,6,0,13
K03455	5156	.	T	A	.	.	DP=28;ECNT=27;MBQ=38,37;MFRL=315,181;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=16.29	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:14,5:0.283:19:0,0:14,5:0|1:5156_T_A:5156:0,14,0,5
K03455	5157	.	T	G	.	.	DP=28;ECNT=27;MBQ=38,37;MFRL=181,331;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=49.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:5,13:0.703:18:0,0:5,13:0,5,0,13
K03455	5169	.	C	T	.	.	DP=20;ECNT=27;MBQ=39,39;MFRL=296,170;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=20.02	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:14,6:0.318:20:0,0:14,6:0,14,0,6
K03455	5175	.	A	T	.	.	DP=19;ECNT=27;MBQ=37,39;MFRL=203,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=34.23	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:10,9:0.476:19:0,0:9,9:0|1:5147_G_A:5147:0,10,0,9
K03455	5177	.	G	C	.	.	DP=18;ECNT=27;MBQ=39,37;MFRL=299,216;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=25.72	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:11,7:0.400:18:0,0:10,7:0|1:5133_T_C:5133:0,11,0,7
K03455	5179	.	CC	AC,AA	.	.	DP=17;ECNT=27;MBQ=39,36,39;MFRL=366,216,315;MMQ=60,60,60;MPOS=60,51;POPAF=7.30,7.30;TLOD=26.12,30.50	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:2,7,8:0.400,0.450:17:0,0,0:2,7,8:0,2,0,15
K03455	5189	.	G	A	.	.	DP=18;ECNT=27;MBQ=39,39;MFRL=203,315;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=30.08	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:10,8:0.450:18:1,0:9,8:1,9,0,8
K03455	5190	.	A	G	.	.	DP=18;ECNT=27;MBQ=39,20;MFRL=293,181;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=9.31	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:15,3:0.200:18:0,0:15,2:0|1:5156_T_A:5156:0,15,1,2
K03455	5196	.	T	C	.	.	DP=18;ECNT=27;MBQ=39,37;MFRL=293,181;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=9.19	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:15,3:0.200:18:0,1:15,2:0,15,1,2
K03455	5220	.	G	A	.	.	DP=16;ECNT=27;MBQ=38,38;MFRL=312,219;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=21.54	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:10,6:0.389:16:1,0:9,6:0|1:5220_G_A:5220:1,9,0,6
K03455	5223	.	T	A	.	.	DP=16;ECNT=27;MBQ=37,39;MFRL=293,181;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.40	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,3:0.222:16:0,1:13,2:0|1:5223_T_A:5223:0,13,1,2
K03455	5230	.	T	C	.	.	DP=16;ECNT=27;MBQ=38,39;MFRL=293,181;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=9.40	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,3:0.222:16:0,1:12,2:0|1:5223_T_A:5223:0,13,1,2
K03455	5233	.	G	A	.	.	DP=12;ECNT=27;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=18.49	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:7,5:0.429:12:0,0:6,5:0|1:5220_G_A:5220:1,6,0,5
K03455	5236	.	A	G	.	.	DP=12;ECNT=27;MBQ=37,38;MFRL=216,256;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=22.57	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:5,6:0.539:11:0,1:5,5:0,5,1,5
K03455	5240	.	C	T	.	.	DP=11;ECNT=27;MBQ=37,37;MFRL=219,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.66	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:8,3:0.308:11:0,0:7,3:1,7,0,3