Mercurial > repos > iuc > vardict_java

comparison test-data/passed_variants_single.vcf @ 2:d262577e04b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e"
author iuc
date Tue, 16 Nov 2021 19:05:56 +0000
parents 5f756651a1bc
children
comparison
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1:5f756651a1bc 2:d262577e04b0
1 ##fileformat=VCFv4.3 1 ##fileformat=VCFv4\.2
2 ##source=VarDict_v1.8.1 2 ##source=VarDict_v\d\.[.0-9]+
3 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)"> 3 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="[^"]+">
4 ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex"> 4 ##INFO=<ID=TYPE,Number=1,Type=String,Description="[^"]+">
5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> 5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="[^"]+">
6 ##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position"> 6 ##INFO=<ID=END,Number=1,Type=Integer,Description="[^"]+">
7 ##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth"> 7 ##INFO=<ID=VD,Number=1,Type=Integer,Description="[^"]+">
8 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> 8 ##INFO=<ID=AF,Number=A,Type=Float,Description="[^"]+">
9 ##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info"> 9 ##INFO=<ID=BIAS,Number=1,Type=String,Description="[^"]+">
10 ##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand"> 10 ##INFO=<ID=REFBIAS,Number=1,Type=String,Description="[^"]+">
11 ##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand"> 11 ##INFO=<ID=VARBIAS,Number=1,Type=String,Description="[^"]+">
12 ##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads"> 12 ##INFO=<ID=PMEAN,Number=1,Type=Float,Description="[^"]+">
13 ##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads"> 13 ##INFO=<ID=PSTD,Number=1,Type=Float,Description="[^"]+">
14 ##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads"> 14 ##INFO=<ID=QUAL,Number=1,Type=Float,Description="[^"]+">
15 ##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads"> 15 ##INFO=<ID=QSTD,Number=1,Type=Float,Description="[^"]+">
16 ##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value"> 16 ##INFO=<ID=SBF,Number=1,Type=Float,Description="[^"]+">
17 ##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio"> 17 ##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="[^"]+">
18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality"> 18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="[^"]+">
19 ##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise"> 19 ##INFO=<ID=SN,Number=1,Type=Float,Description="[^"]+">
20 ##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases"> 20 ##INFO=<ID=HIAF,Number=1,Type=Float,Description="[^"]+">
21 ##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment"> 21 ##INFO=<ID=ADJAF,Number=1,Type=Float,Description="[^"]+">
22 ##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment"> 22 ##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="[^"]+">
23 ##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI"> 23 ##INFO=<ID=MSI,Number=1,Type=Float,Description="[^"]+">
24 ##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp"> 24 ##INFO=<ID=MSILEN,Number=1,Type=Float,Description="[^"]+">
25 ##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads"> 25 ##INFO=<ID=NM,Number=1,Type=Float,Description="[^"]+">
26 ##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq"> 26 ##INFO=<ID=LSEQ,Number=1,Type=String,Description="[^"]+">
27 ##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq"> 27 ##INFO=<ID=RSEQ,Number=1,Type=String,Description="[^"]+">
28 ##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant"> 28 ##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="[^"]+">
29 ##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant"> 29 ##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="[^"]+">
30 ##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don't work"> 30 ##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="[^"]+">
31 ##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don't match"> 31 ##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="[^"]+">
32 ##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads"> 32 ##INFO=<ID=HICNT,Number=1,Type=Integer,Description="[^"]+">
33 ##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads"> 33 ##INFO=<ID=HICOV,Number=1,Type=Integer,Description="[^"]+">
34 ##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV"> 34 ##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="[^"]+">
35 ##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV"> 35 ##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="[^"]+">
36 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS"> 36 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="[^"]+">
37 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp"> 37 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="[^"]+">
38 ##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction"> 38 ##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="[^"]+">
39 ##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5"> 39 ##FILTER=<ID=q22\.5,Description="[^"]+">
40 ##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10"> 40 ##FILTER=<ID=Q10,Description="[^"]+">
41 ##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8"> 41 ##FILTER=<ID=p8,Description="[^"]+">
42 ##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5"> 42 ##FILTER=<ID=SN1\.5,Description="[^"]+">
43 ##FILTER=<ID=Bias,Description="Strand Bias"> 43 ##FILTER=<ID=Bias,Description="[^"]+">
44 ##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0"> 44 ##FILTER=<ID=pSTD,Description="[^"]+">
45 ##FILTER=<ID=d3,Description="Total Depth < 3"> 45 ##FILTER=<ID=d3,Description="[^"]+">
46 ##FILTER=<ID=v2,Description="Var Depth < 2"> 46 ##FILTER=<ID=v2,Description="[^"]+">
47 ##FILTER=<ID=f0.01,Description="Allele frequency < 0.01"> 47 ##FILTER=<ID=f0\.01,Description="[^"]+">
48 ##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI"> 48 ##FILTER=<ID=MSI12,Description="[^"]+">
49 ##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive"> 49 ##FILTER=<ID=NM5\.25,Description="[^"]+">
50 ##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive"> 50 ##FILTER=<ID=InGap,Description="[^"]+">
51 ##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant"> 51 ##FILTER=<ID=InIns,Description="[^"]+">
52 ##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp"> 52 ##FILTER=<ID=Cluster0bp,Description="[^"]+">
53 ##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)"> 53 ##FILTER=<ID=LongMSI,Description="[^"]+">
54 ##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias."> 54 ##FILTER=<ID=AMPBIAS,Description="[^"]+">
55 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 55 ##FORMAT=<ID=GT,Number=1,Type=String,Description="[^"]+">
56 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> 56 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="[^"]+">
57 ##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth"> 57 ##FORMAT=<ID=VD,Number=1,Type=Integer,Description="[^"]+">
58 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 58 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="[^"]+">
59 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> 59 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="[^"]+">
60 ##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads"> 60 ##FORMAT=<ID=RD,Number=2,Type=Integer,Description="[^"]+">
61 ##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads"> 61 ##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="[^"]+">
62 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample 62 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample
63 chrM 150 . T C 40 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:2;PMEAN=35;PSTD=1;QUAL=40.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:0,2 63 chrM 150 \. T C 40 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:2;PMEAN=35;PSTD=1;QUAL=40.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:0,2
64 chrM 410 . A T 58 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=3:0;PMEAN=23.3;PSTD=1;QUAL=36.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;NM=2.3;HICNT=3;HICOV=3;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:3,0 64 chrM 410 \. A T 58 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=3:0;PMEAN=23.3;PSTD=1;QUAL=36.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;NM=2.3;HICNT=3;HICOV=3;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:3,0
65 chrM 464 . C T 108 PASS SAMPLE=Sample;TYPE=SNV;DP=8;VD=8;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=6:2;PMEAN=22.8;PSTD=1;QUAL=36.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=16;HIAF=1.0000;ADJAF=0;SHIFT3=2;MSI=3;MSILEN=1;NM=2.1;HICNT=8;HICOV=8;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:8:8:0,8:1:0,0:6,2 65 chrM 464 \. C T 108 PASS SAMPLE=Sample;TYPE=SNV;DP=8;VD=8;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=6:2;PMEAN=22.8;PSTD=1;QUAL=36.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=16;HIAF=1.0000;ADJAF=0;SHIFT3=2;MSI=3;MSILEN=1;NM=2.1;HICNT=8;HICOV=8;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:8:8:0,8:1:0,0:6,2
66 chrM 491 . T C 127 PASS SAMPLE=Sample;TYPE=SNV;DP=10;VD=10;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=8:2;PMEAN=28.3;PSTD=1;QUAL=38.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=20;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.7;HICNT=10;HICOV=10;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:10:10:0,10:1:0,0:8,2 66 chrM 491 \. T C 127 PASS SAMPLE=Sample;TYPE=SNV;DP=10;VD=10;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=8:2;PMEAN=28.3;PSTD=1;QUAL=38.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=20;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.7;HICNT=10;HICOV=10;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:10:10:0,10:1:0,0:8,2
67 chrM 681 . C T 30 PASS SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=70:52;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.34287;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:124:2:122,2:0.0161:70,52:1,1 67 chrM 681 \. C T 30 PASS SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=70:52;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.34287;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:124:2:122,2:0.0161:70,52:1,1
68 chrM 692 . T C 38 PASS SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=73:49;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=1.48485;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:124:2:122,2:0.0161:73,49:1,1 68 chrM 692 \. T C 38 PASS SAMPLE=Sample;TYPE=SNV;DP=124;VD=2;AF=0.0161;BIAS=2:2;REFBIAS=73:49;VARBIAS=1:1;PMEAN=36;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=1.48485;MQ=49;SN=4;HIAF=0.0163;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=123;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:124:2:122,2:0.0161:73,49:1,1
69 chrM 737 . A G 30 PASS SAMPLE=Sample;TYPE=SNV;DP=106;VD=2;AF=0.0189;BIAS=2:2;REFBIAS=42:61;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.44707329426235;MQ=60;SN=4;HIAF=0.0202;ADJAF=0.0094;SHIFT3=1;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=99;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:106:2:103,2:0.0189:42,61:1,1 69 chrM 737 \. A G 30 PASS SAMPLE=Sample;TYPE=SNV;DP=106;VD=2;AF=0.0189;BIAS=2:2;REFBIAS=42:61;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=30.5;QSTD=1;SBF=1;ODDRATIO=1.44707329426235;MQ=60;SN=4;HIAF=0.0202;ADJAF=0.0094;SHIFT3=1;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=99;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:106:2:103,2:0.0189:42,61:1,1
70 chrM 1735 . C T 63 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:2;PMEAN=46.7;PSTD=1;QUAL=40.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=3;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:1,2 70 chrM 1735 \. C T 63 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:2;PMEAN=46.7;PSTD=1;QUAL=40.3;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=3;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:1,2
71 chrM 2354 . C T 57 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=18.3;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=4;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:2,1 71 chrM 2354 \. C T 57 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=18.3;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=6;HIAF=1.0000;ADJAF=0.3333;SHIFT3=0;MSI=4;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:2,1
72 chrM 2485 . C T 59 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=17.7;PSTD=1;QUAL=37.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=53.3;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:2,1 72 chrM 2485 \. C T 59 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:1;PMEAN=17.7;PSTD=1;QUAL=37.7;QSTD=1;SBF=1;ODDRATIO=0;MQ=53.3;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:2,1
73 chrM 6720 . T C 75 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=56;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2 73 chrM 6720 \. T C 75 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=56;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2
74 chrM 8702 . G A 34 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=46;PSTD=1;QUAL=34;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 74 chrM 8702 \. G A 34 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=46;PSTD=1;QUAL=34;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
75 chrM 9378 . G A 57 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:3;PMEAN=20.3;PSTD=1;QUAL=36;QSTD=1;SBF=1;ODDRATIO=0;MQ=46;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:0,3 75 chrM 9378 \. G A 57 PASS SAMPLE=Sample;TYPE=SNV;DP=3;VD=3;AF=1;BIAS=0:0;REFBIAS=0:0;VARBIAS=0:3;PMEAN=20.3;PSTD=1;QUAL=36;QSTD=1;SBF=1;ODDRATIO=0;MQ=46;SN=6;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=3;HICOV=3;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:3:3:0,3:1:0,0:0,3
76 chrM 9541 . C T 37 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=48.5;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 76 chrM 9541 \. C T 37 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=48.5;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
77 chrM 10874 . C T 37 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=30;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=5;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 77 chrM 10874 \. C T 37 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=30;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=5;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
78 chrM 11198 . C A 31 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=2;AF=0.2222;BIAS=2:2;REFBIAS=3:4;VARBIAS=1:1;PMEAN=31.5;PSTD=1;QUAL=31.5;QSTD=1;SBF=1;ODDRATIO=1.29098889749548;MQ=60;SN=4;HIAF=0.2222;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=2;NM=1.5;HICNT=2;HICOV=9;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:9:2:7,2:0.2222:3,4:1,1 78 chrM 11198 \. C A 31 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=2;AF=0.2222;BIAS=2:2;REFBIAS=3:4;VARBIAS=1:1;PMEAN=31.5;PSTD=1;QUAL=31.5;QSTD=1;SBF=1;ODDRATIO=1.29098889749548;MQ=60;SN=4;HIAF=0.2222;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=2;NM=1.5;HICNT=2;HICOV=9;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:9:2:7,2:0.2222:3,4:1,1
79 chrM 11252 . A G 86 PASS SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:4;PMEAN=26.2;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=10;HIAF=1.0000;ADJAF=0.2;SHIFT3=0;MSI=2;MSILEN=1;NM=1.2;HICNT=5;HICOV=5;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:5:5:0,5:1:0,0:1,4 79 chrM 11252 \. A G 86 PASS SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:4;PMEAN=26.2;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=10;HIAF=1.0000;ADJAF=0.2;SHIFT3=0;MSI=2;MSILEN=1;NM=1.2;HICNT=5;HICOV=5;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:5:5:0,5:1:0,0:1,4
80 chrM 11464 . T A 32 PASS SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=25.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:6:2:4,2:0.3333:2,2:1,1 80 chrM 11464 \. T A 32 PASS SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=25.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:6:2:4,2:0.3333:2,2:1,1
81 chrM 12851 . G A 73 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=22.5;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2 81 chrM 12851 \. G A 73 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=22.5;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2
82 chrM 13709 . G A 32 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 82 chrM 13709 \. G A 32 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
83 chrM 14581 . G A 86 PASS SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:5:5:0,5:1:0,0:3,2 83 chrM 14581 \. G A 86 PASS SAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:5:5:0,5:1:0,0:3,2
84 chrM 14794 . A G 37 PASS SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:6:2:4,2:0.3333:2,2:1,1 84 chrM 14794 \. A G 37 PASS SAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 0/1:6:2:4,2:0.3333:2,2:1,1
85 chrM 14906 . A G 108 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:9:9:0,9:1:0,0:5,4 85 chrM 14906 \. A G 108 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:9:9:0,9:1:0,0:5,4
86 chrM 14928 . A G 122 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:9:9:0,9:1:0,0:5,4 86 chrM 14928 \. A G 122 PASS SAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:9:9:0,9:1:0,0:5,4
87 chrM 15302 . A G 38 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 87 chrM 15302 \. A G 38 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
88 chrM 16263 . C T 68 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2 88 chrM 16263 \. C T 68 PASS SAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:4:4:0,4:1:0,0:2,2
89 chrM 16322 . T C 33 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 89 chrM 16322 \. T C 33 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1
90 chrM 16521 . C T 38 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1 90 chrM 16521 \. C T 38 PASS SAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0 GT:DP:VD:AD:AF:RD:ALD 1/1:2:2:0,2:1:0,0:1,1