Mercurial > repos > jpayne > snp_pipeline

view test-data/samples/sample2/consensus.vcf @ 64:b5cf2ec0c540 tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jpayne
date Sat, 29 Jun 2024 06:56:11 -0400
parents eefdd97a6749
children
line wrap: on
line source
##fileformat=VCFv4.1
##fileDate=20180103
##source=CFSAN SNP-Pipeline 1.0.1
##reference=lambda_virus.fasta
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=RawDpth,Description="No read depth">
##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample2
gi|9626243|ref|NC_001416.1|	403	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	550	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	586	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	753	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:10:17:0:0:PASS
gi|9626243|ref|NC_001416.1|	1019	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	1079	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
gi|9626243|ref|NC_001416.1|	1540	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:3:19:0:0:PASS
gi|9626243|ref|NC_001416.1|	1620	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:10:1:0:10:0:1:PASS
gi|9626243|ref|NC_001416.1|	1650	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:9:0:0:9:0:0:PASS
gi|9626243|ref|NC_001416.1|	1788	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:8:8:0:8:0:0:0:PASS
gi|9626243|ref|NC_001416.1|	1804	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:11:0:10:1:0:0:PASS
gi|9626243|ref|NC_001416.1|	2123	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:10:10:0:0:PASS
gi|9626243|ref|NC_001416.1|	2439	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:10:6:0:0:PASS
gi|9626243|ref|NC_001416.1|	2452	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:11:10:1:0:PASS
gi|9626243|ref|NC_001416.1|	2599	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:8:17:PASS
gi|9626243|ref|NC_001416.1|	3063	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:16:9:0:1:PASS
gi|9626243|ref|NC_001416.1|	3351	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:30:1:12:18:0:1:PASS
gi|9626243|ref|NC_001416.1|	3648	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:10:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	3656	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:8:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	3678	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:1:18:1:0:10:8:PASS
gi|9626243|ref|NC_001416.1|	4977	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:12:17:1:0:PASS
gi|9626243|ref|NC_001416.1|	5142	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:4:14:PASS
gi|9626243|ref|NC_001416.1|	5336	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:8:0:8:0:0:1:7:PASS
gi|9626243|ref|NC_001416.1|	5462	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:9:9:0:9:0:0:0:PASS
gi|9626243|ref|NC_001416.1|	5482	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:10:2:10:0:2:0:PASS
gi|9626243|ref|NC_001416.1|	5516	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:10:1:10:0:1:0:PASS
gi|9626243|ref|NC_001416.1|	5800	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:16:7:0:0:PASS
gi|9626243|ref|NC_001416.1|	5818	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	5994	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
gi|9626243|ref|NC_001416.1|	6296	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:10:14:0:0:PASS
gi|9626243|ref|NC_001416.1|	6535	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:8:13:PASS
gi|9626243|ref|NC_001416.1|	6824	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:23:1:8:15:1:0:PASS
gi|9626243|ref|NC_001416.1|	7424	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:15:9:PASS
gi|9626243|ref|NC_001416.1|	7668	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	7897	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:9:17:0:0:PASS
gi|9626243|ref|NC_001416.1|	8420	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:11:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	8938	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:12:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	9175	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:13:12:1:3:9:0:1:PASS
gi|9626243|ref|NC_001416.1|	9234	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	9919	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	10127	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:17:15:PASS
gi|9626243|ref|NC_001416.1|	10264	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	10421	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:22:8:0:0:PASS
gi|9626243|ref|NC_001416.1|	10568	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	11066	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:11:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	11128	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:11:17:0:0:PASS
gi|9626243|ref|NC_001416.1|	11782	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:7:10:PASS
gi|9626243|ref|NC_001416.1|	12070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:9:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	12717	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:7:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	12795	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	12876	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:25:0:14:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	12959	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:8:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	12970	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:9:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	13107	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:7:13:1:0:PASS
gi|9626243|ref|NC_001416.1|	13264	.	C	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:23:0:23:0:0:15:8:PASS
gi|9626243|ref|NC_001416.1|	13542	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:25:0:0:16:9:PASS
gi|9626243|ref|NC_001416.1|	13647	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:15:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	13952	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:33:0:33:0:0:14:19:PASS
gi|9626243|ref|NC_001416.1|	13971	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	15384	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:14:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	15715	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:24:0:24:0:0:17:7:PASS
gi|9626243|ref|NC_001416.1|	15967	.	A	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:26:0:0:14:12:PASS
gi|9626243|ref|NC_001416.1|	16070	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:19:8:0:0:PASS
gi|9626243|ref|NC_001416.1|	16654	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:20:20:0:8:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	16715	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:14:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	17142	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:14:13:PASS
gi|9626243|ref|NC_001416.1|	17311	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:35:0:35:0:0:15:20:PASS
gi|9626243|ref|NC_001416.1|	17854	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:6:14:PASS
gi|9626243|ref|NC_001416.1|	18151	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:27:0:16:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	18188	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:14:17:0:0:PASS
gi|9626243|ref|NC_001416.1|	18210	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:28:2:13:15:0:2:PASS
gi|9626243|ref|NC_001416.1|	18420	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:18:0:18:0:0:10:8:PASS
gi|9626243|ref|NC_001416.1|	18598	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:27:1:14:13:0:1:PASS
gi|9626243|ref|NC_001416.1|	18652	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:15:10:PASS
gi|9626243|ref|NC_001416.1|	18989	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:15:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	19208	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:17:0:17:0:0:9:8:PASS
gi|9626243|ref|NC_001416.1|	19448	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:14:18:0:0:PASS
gi|9626243|ref|NC_001416.1|	19469	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:12:18:0:0:PASS
gi|9626243|ref|NC_001416.1|	20079	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
gi|9626243|ref|NC_001416.1|	20099	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:16:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	20289	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:34:34:0:19:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	20367	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:20:12:PASS
gi|9626243|ref|NC_001416.1|	21110	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:20:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	21320	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:12:13:PASS
gi|9626243|ref|NC_001416.1|	21653	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:22:1:8:14:1:0:PASS
gi|9626243|ref|NC_001416.1|	22220	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:28:0:0:17:11:PASS
gi|9626243|ref|NC_001416.1|	22357	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:17:17:0:6:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	22747	.	G	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:19:0:0:7:12:PASS
gi|9626243|ref|NC_001416.1|	23362	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:9:11:1:0:PASS
gi|9626243|ref|NC_001416.1|	23457	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19:0:0:12:7:PASS
gi|9626243|ref|NC_001416.1|	24043	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	24319	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:9:11:1:0:PASS
gi|9626243|ref|NC_001416.1|	24766	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	24930	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:15:0:8:7:0:0:PASS
gi|9626243|ref|NC_001416.1|	25005	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:12:0:12:0:0:6:6:PASS
gi|9626243|ref|NC_001416.1|	25158	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:11:11:PASS
gi|9626243|ref|NC_001416.1|	25645	.	C	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:26:0:0:11:15:PASS
gi|9626243|ref|NC_001416.1|	26173	.	G	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
gi|9626243|ref|NC_001416.1|	26728	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	26972	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:11:14:1:0:PASS
gi|9626243|ref|NC_001416.1|	27412	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:13:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	27539	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:13:18:0:0:PASS
gi|9626243|ref|NC_001416.1|	27661	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24:0:0:14:10:PASS
gi|9626243|ref|NC_001416.1|	27722	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:29:1:12:17:1:0:PASS
gi|9626243|ref|NC_001416.1|	27790	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:13:13:1:0:PASS
gi|9626243|ref|NC_001416.1|	27825	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:14:9:0:0:PASS
gi|9626243|ref|NC_001416.1|	27834	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:18:14:0:0:PASS
gi|9626243|ref|NC_001416.1|	28045	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:13:12:PASS
gi|9626243|ref|NC_001416.1|	28362	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:22:0:0:12:10:PASS
gi|9626243|ref|NC_001416.1|	29265	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:13:8:0:0:PASS
gi|9626243|ref|NC_001416.1|	29411	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:31:0:31:0:0:15:16:PASS
gi|9626243|ref|NC_001416.1|	29435	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:27:2:12:15:1:1:PASS
gi|9626243|ref|NC_001416.1|	29891	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
gi|9626243|ref|NC_001416.1|	30125	.	A	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:11:10:PASS
gi|9626243|ref|NC_001416.1|	30757	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:9:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	30890	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:11:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	31328	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:11:10:0:0:PASS
gi|9626243|ref|NC_001416.1|	31363	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:22:0:10:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	31551	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:10:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	32086	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:10:15:0:1:PASS
gi|9626243|ref|NC_001416.1|	32660	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:20:1:12:8:1:0:PASS
gi|9626243|ref|NC_001416.1|	33000	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:15:14:1:10:4:1:0:PASS
gi|9626243|ref|NC_001416.1|	33591	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:25:1:11:14:1:0:PASS
gi|9626243|ref|NC_001416.1|	33612	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:25:24:1:8:16:1:0:PASS
gi|9626243|ref|NC_001416.1|	33865	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:24:24:0:11:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	34137	.	T	G	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:34:0:33:0:0:18:15:PASS
gi|9626243|ref|NC_001416.1|	34370	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:12:19:0:0:PASS
gi|9626243|ref|NC_001416.1|	34812	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:18:18:0:7:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	34920	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:12:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	35148	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:13:15:0:0:PASS
gi|9626243|ref|NC_001416.1|	35802	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:15:8:0:0:PASS
gi|9626243|ref|NC_001416.1|	35907	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:30:0:0:19:11:PASS
gi|9626243|ref|NC_001416.1|	36010	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:28:28:0:12:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	36169	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:15:13:0:1:PASS
gi|9626243|ref|NC_001416.1|	36642	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:14:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	37208	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:19:7:0:0:PASS
gi|9626243|ref|NC_001416.1|	37387	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:13:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	37519	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:10:9:0:0:PASS
gi|9626243|ref|NC_001416.1|	37898	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:14:14:1:0:PASS
gi|9626243|ref|NC_001416.1|	38073	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:27:26:1:15:11:0:1:PASS
gi|9626243|ref|NC_001416.1|	38165	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:18:1:14:4:0:1:PASS
gi|9626243|ref|NC_001416.1|	38575	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:21:0:21:0:0:10:11:PASS
gi|9626243|ref|NC_001416.1|	39003	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:16:16:0:6:10:0:0:PASS
gi|9626243|ref|NC_001416.1|	39206	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19:0:0:7:12:PASS
gi|9626243|ref|NC_001416.1|	39484	.	C	A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:20:0:0:12:8:PASS
gi|9626243|ref|NC_001416.1|	39485	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:21:21:0:14:7:0:0:PASS
gi|9626243|ref|NC_001416.1|	40457	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:31:1:15:16:1:0:PASS
gi|9626243|ref|NC_001416.1|	40835	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:33:33:0:17:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	40984	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:7:12:0:0:PASS
gi|9626243|ref|NC_001416.1|	41064	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:31:31:0:17:14:0:0:PASS
gi|9626243|ref|NC_001416.1|	41448	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:12:14:0:0:PASS
gi|9626243|ref|NC_001416.1|	41954	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:32:32:0:16:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	42439	.	A	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:23:23:0:13:10:0:0:PASS
gi|9626243|ref|NC_001416.1|	43306	.	T	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:29:0:13:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	43470	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:25:0:0:14:11:PASS
gi|9626243|ref|NC_001416.1|	44134	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21:0:0:12:9:PASS
gi|9626243|ref|NC_001416.1|	44201	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:30:30:0:13:17:0:0:PASS
gi|9626243|ref|NC_001416.1|	44413	.	G	T	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:32:0:0:13:19:PASS
gi|9626243|ref|NC_001416.1|	45364	.	A	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:25:0:0:16:9:PASS
gi|9626243|ref|NC_001416.1|	45409	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:26:26:0:13:13:0:0:PASS
gi|9626243|ref|NC_001416.1|	46237	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:19:19:0:3:16:0:0:PASS
gi|9626243|ref|NC_001416.1|	46283	.	C	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:12:12:0:1:11:0:0:PASS
gi|9626243|ref|NC_001416.1|	46842	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:29:28:1:12:16:1:0:PASS
gi|9626243|ref|NC_001416.1|	47425	.	T	C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:18:0:0:11:7:PASS
gi|9626243|ref|NC_001416.1|	47893	.	G	.	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:11:11:0:5:6:0:0:PASS