annotate test-data/passed_variants_single.vcf @ 0:2975b29bcaa1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"

##fileformat=VCFv4.1
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">
##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">
##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">
##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">
##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">
##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don't work">
##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don't match">
##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">
##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">
##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">
##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">
##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">
##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
##FILTER=<ID=Bias,Description="Strand Bias">
##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
##FILTER=<ID=d3,Description="Total Depth < 3">
##FILTER=<ID=v2,Description="Var Depth < 2">
##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">
##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">
##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">
##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">
##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">
##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp">
##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)">
##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##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 Frequency">
##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">
##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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