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author greg
date Thu, 23 Nov 2023 22:11:08 +0000
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##fileformat=VCFv4.2
##fileDate=20231013
##source=CFSAN SNP-Pipeline 2.2.1
##reference=Unknown reference
##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">
##FORMAT=<ID=AD,Number=A,Type=Integer,Description="Depth of variant-supporting bases (comma-separated depth per alt allele)">
##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand">
##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand">
##FORMAT=<ID=ADF,Number=A,Type=Integer,Description="Depth of variant-supporting bases on forward strand (comma-separated depth per alt allele)">
##FORMAT=<ID=ADR,Number=A,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (comma-separated depth per alt allele)">
##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=Depth1,Description="Less than 1 supporting reads">
##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	f
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|	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|	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|	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|	6535	.	C	A,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21,1:0:0:8,1:13,0:PASS
gi|9626243|ref|NC_001416.1|	7424	.	G	T,C	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24,1:0:0:15,0:9,1: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|	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|	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,A	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:26:0:25,1:0:0:16,0:9,1: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|	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,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:28:0:26,2:0:0:14,1:12,1: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|	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|	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|	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|	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|	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|	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|	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|	23457	.	A	C,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19,1:0:0:12,1:7,0: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|	27661	.	T	C,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:25:0:24,1:0:0:14,1:10,0: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|	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|	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|	34137	.	T	G,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:34:0:33,1:0:0:18,1:15,0:PASS
gi|9626243|ref|NC_001416.1|	35907	.	G	T,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:32:0:30,2:0:0:19,1:11,1: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|	39206	.	T	C,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:20:0:19,1:0:0:7,1:12,0: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|	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,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:22:0:21,1:0:0:12,0:9,1: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,G,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:25,1,1:0:0:16,1,1:9,0,0:PASS
gi|9626243|ref|NC_001416.1|	47425	.	T	C,N	.	PASS	NS=1	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:19:0:18,1:0:0:11,0:7,1:PASS