Mercurial > repos > jpayne > snp_pipeline
view test-data/samples/sample2/consensus.vcf @ 10:25b858c2f21d
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
| author | jpayne |
|---|---|
| date | Tue, 30 Jan 2018 17:14:23 -0500 |
| 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