jpayne@58: ##fileformat=VCFv4.1
jpayne@58: ##source=VarScan2
jpayne@58: ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
jpayne@58: ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
jpayne@58: ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
jpayne@58: ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
jpayne@58: ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
jpayne@58: ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
jpayne@58: ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
jpayne@58: ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
jpayne@58: ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
jpayne@58: ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
jpayne@58: ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
jpayne@58: ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
jpayne@58: ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
jpayne@58: ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
jpayne@58: ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
jpayne@58: ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
jpayne@58: ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
jpayne@58: ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
jpayne@58: ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
jpayne@58: ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
jpayne@58: ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
jpayne@58: #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
jpayne@58: gi|9626243|ref|NC_001416.1|	753	.	G	A	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:25:24:0:23:100%:1.2146E-13:0:27:0:0:15:8
jpayne@58: gi|9626243|ref|NC_001416.1|	1079	.	T	C	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:26:25:0:24:100%:3.101E-14:0:26:0:0:9:15
jpayne@58: gi|9626243|ref|NC_001416.1|	1540	.	A	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:24:22:0:22:100%:4.7526E-13:0:24:0:0:13:9
jpayne@58: gi|9626243|ref|NC_001416.1|	1804	.	G	C	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:23:23:0:23:100%:1.2146E-13:0:28:0:0:11:12
jpayne@58: gi|9626243|ref|NC_001416.1|	2123	.	G	C	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:24:23:0:23:100%:1.2146E-13:0:27:0:0:10:13
jpayne@58: gi|9626243|ref|NC_001416.1|	3351	.	C	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:24:22:0:22:100%:4.7526E-13:0:28:0:0:10:12
jpayne@58: gi|9626243|ref|NC_001416.1|	3656	.	T	G	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:12:11
jpayne@58: gi|9626243|ref|NC_001416.1|	6824	.	A	C	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:10:8
jpayne@58: gi|9626243|ref|NC_001416.1|	7897	.	G	A	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:26:23:0:23:100%:1.2146E-13:0:25:0:0:11:12
jpayne@58: gi|9626243|ref|NC_001416.1|	9175	.	A	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:22:22:0:22:100%:4.7526E-13:0:28:0:0:8:14
jpayne@58: gi|9626243|ref|NC_001416.1|	12717	.	G	C	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:29:25:0:24:100%:3.101E-14:0:28:0:0:10:14
jpayne@58: gi|9626243|ref|NC_001416.1|	12795	.	C	T	.	PASS	ADP=26;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:146:27:26:0:26:100%:2.0165E-15:0:29:0:0:16:10
jpayne@58: gi|9626243|ref|NC_001416.1|	12959	.	T	G	.	PASS	ADP=21;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:117:22:21:0:21:100%:1.8578E-12:0:25:0:0:13:8
jpayne@58: gi|9626243|ref|NC_001416.1|	16654	.	C	G	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:14:9
jpayne@58: gi|9626243|ref|NC_001416.1|	16715	.	T	G	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:25:0:0:8:10
jpayne@58: gi|9626243|ref|NC_001416.1|	18598	.	C	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:25:22:0:22:100%:4.7526E-13:0:24:0:0:12:10
jpayne@58: gi|9626243|ref|NC_001416.1|	19469	.	G	T	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:21:18:0:18:100%:1.1019E-10:0:28:0:0:11:7
jpayne@58: gi|9626243|ref|NC_001416.1|	20099	.	C	T	.	PASS	ADP=28;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:158:28:28:0:28:100%:1.3074E-16:0:29:0:0:14:14
jpayne@58: gi|9626243|ref|NC_001416.1|	21110	.	T	G	.	PASS	ADP=16;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:87:18:16:0:16:100%:1.6637E-9:0:26:0:0:5:11
jpayne@58: gi|9626243|ref|NC_001416.1|	23362	.	T	A	.	PASS	ADP=11;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:58:14:11:0:11:100%:1.4176E-6:0:26:0:0:3:8
jpayne@58: gi|9626243|ref|NC_001416.1|	24319	.	G	T	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11
jpayne@58: gi|9626243|ref|NC_001416.1|	24766	.	G	A	.	PASS	ADP=17;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:19:17:0:17:100%:4.2852E-10:0:24:0:0:6:11
jpayne@58: gi|9626243|ref|NC_001416.1|	27790	.	A	C	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:20:18:0:17:100%:4.2852E-10:0:26:0:0:6:11
jpayne@58: gi|9626243|ref|NC_001416.1|	29891	.	G	C	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:21:20:0:20:100%:7.2544E-12:0:26:0:0:9:11
jpayne@58: gi|9626243|ref|NC_001416.1|	31551	.	A	G	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:81:16:15:0:15:100%:6.4467E-9:0:25:0:0:7:8
jpayne@58: gi|9626243|ref|NC_001416.1|	32086	.	T	A	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:69:17:15:1:14:93.33%:1.0315E-7:33:28:1:0:7:7
jpayne@58: gi|9626243|ref|NC_001416.1|	33000	.	C	T	.	PASS	ADP=17;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:18:17:0:17:100%:4.2852E-10:0:26:0:0:7:10
jpayne@58: gi|9626243|ref|NC_001416.1|	33591	.	T	G	.	PASS	ADP=30;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:170:30:30:0:30:100%:8.4556E-18:0:26:0:0:16:14
jpayne@58: gi|9626243|ref|NC_001416.1|	36010	.	C	T	.	PASS	ADP=9;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:46:9:9:0:9:100%:2.0568E-5:0:26:0:0:0:9
jpayne@58: gi|9626243|ref|NC_001416.1|	37208	.	G	C	.	PASS	ADP=19;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:105:19:19:0:19:100%:2.8292E-11:0:29:0:0:8:11
jpayne@58: gi|9626243|ref|NC_001416.1|	38165	.	T	C	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:152:29:27:0:27:100%:5.1363E-16:0:23:0:0:17:10
jpayne@58: gi|9626243|ref|NC_001416.1|	39485	.	A	C	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:20:20:0:20:100%:7.2544E-12:0:29:0:0:10:10
jpayne@58: gi|9626243|ref|NC_001416.1|	40457	.	T	C	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:138:28:27:1:26:96.3%:1.4382E-14:24:25:1:0:11:15
jpayne@58: gi|9626243|ref|NC_001416.1|	42439	.	A	C	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:28:24:0:24:100%:3.101E-14:0:26:0:0:16:8
jpayne@58: gi|9626243|ref|NC_001416.1|	43306	.	T	G	.	PASS	ADP=32;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:176:33:32:0:31:100%:2.1486E-18:0:27:0:0:11:20
jpayne@58: gi|9626243|ref|NC_001416.1|	46237	.	G	A	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:152:27:27:0:27:100%:5.1363E-16:0:26:0:0:12:15
jpayne@58: gi|9626243|ref|NC_001416.1|	47893	.	G	A	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:28:23:0:23:100%:1.2146E-13:0:25:0:0:12:11