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annotate test-data/samples/sample1/consensus.vcf @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents eefdd97a6749
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jpayne@0 1 ##fileformat=VCFv4.1
jpayne@0 2 ##fileDate=20180103
jpayne@0 3 ##source=CFSAN SNP-Pipeline 1.0.1
jpayne@0 4 ##reference=lambda_virus.fasta
jpayne@0 5 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
jpayne@0 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
jpayne@0 7 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
jpayne@0 8 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
jpayne@0 9 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
jpayne@0 10 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
jpayne@0 11 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
jpayne@0 12 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
jpayne@0 13 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
jpayne@0 14 ##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
jpayne@0 15 ##FILTER=<ID=PASS,Description="All filters passed">
jpayne@0 16 ##FILTER=<ID=RawDpth,Description="No read depth">
jpayne@0 17 ##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
jpayne@0 18 ##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
jpayne@0 19 ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
jpayne@0 20 ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
jpayne@0 21 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
jpayne@0 22 gi|9626243|ref|NC_001416.1| 403 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:13:14:PASS
jpayne@0 23 gi|9626243|ref|NC_001416.1| 550 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:13:8:0:1:PASS
jpayne@0 24 gi|9626243|ref|NC_001416.1| 586 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:12:6:0:0:PASS
jpayne@0 25 gi|9626243|ref|NC_001416.1| 753 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24:0:0:16:8:PASS
jpayne@0 26 gi|9626243|ref|NC_001416.1| 1019 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS
jpayne@0 27 gi|9626243|ref|NC_001416.1| 1079 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:25:0:0:9:16:PASS
jpayne@0 28 gi|9626243|ref|NC_001416.1| 1540 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:13:11:PASS
jpayne@0 29 gi|9626243|ref|NC_001416.1| 1620 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS
jpayne@0 30 gi|9626243|ref|NC_001416.1| 1650 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:14:17:0:0:PASS
jpayne@0 31 gi|9626243|ref|NC_001416.1| 1788 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:10:14:0:0:PASS
jpayne@0 32 gi|9626243|ref|NC_001416.1| 1804 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:11:12:PASS
jpayne@0 33 gi|9626243|ref|NC_001416.1| 2123 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:11:13:PASS
jpayne@0 34 gi|9626243|ref|NC_001416.1| 2439 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS
jpayne@0 35 gi|9626243|ref|NC_001416.1| 2452 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:9:9:0:1:PASS
jpayne@0 36 gi|9626243|ref|NC_001416.1| 2599 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:16:12:0:0:PASS
jpayne@0 37 gi|9626243|ref|NC_001416.1| 3063 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:16:10:0:0:PASS
jpayne@0 38 gi|9626243|ref|NC_001416.1| 3351 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:10:14:PASS
jpayne@0 39 gi|9626243|ref|NC_001416.1| 3648 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS
jpayne@0 40 gi|9626243|ref|NC_001416.1| 3656 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:13:12:PASS
jpayne@0 41 gi|9626243|ref|NC_001416.1| 3678 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:7:10:0:0:PASS
jpayne@0 42 gi|9626243|ref|NC_001416.1| 4977 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:12:13:PASS
jpayne@0 43 gi|9626243|ref|NC_001416.1| 5142 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:21:3:11:10:3:0:PASS
jpayne@0 44 gi|9626243|ref|NC_001416.1| 5336 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS
jpayne@0 45 gi|9626243|ref|NC_001416.1| 5462 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:14:11:0:0:PASS
jpayne@0 46 gi|9626243|ref|NC_001416.1| 5482 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:9:9:PASS
jpayne@0 47 gi|9626243|ref|NC_001416.1| 5516 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:9:7:PASS
jpayne@0 48 gi|9626243|ref|NC_001416.1| 5800 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:5:14:PASS
jpayne@0 49 gi|9626243|ref|NC_001416.1| 5818 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:10:15:0:0:PASS
jpayne@0 50 gi|9626243|ref|NC_001416.1| 5994 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:6:9:0:0:PASS
jpayne@0 51 gi|9626243|ref|NC_001416.1| 6296 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:11:8:0:0:PASS
jpayne@0 52 gi|9626243|ref|NC_001416.1| 6535 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS
jpayne@0 53 gi|9626243|ref|NC_001416.1| 6824 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:11:8:PASS
jpayne@0 54 gi|9626243|ref|NC_001416.1| 7424 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:19:1:8:11:0:1:PASS
jpayne@0 55 gi|9626243|ref|NC_001416.1| 7668 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:26:1:17:9:0:1:PASS
jpayne@0 56 gi|9626243|ref|NC_001416.1| 7897 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:13:13:PASS
jpayne@0 57 gi|9626243|ref|NC_001416.1| 8420 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:19:12:0:0:PASS
jpayne@0 58 gi|9626243|ref|NC_001416.1| 8938 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:13:9:0:0:PASS
jpayne@0 59 gi|9626243|ref|NC_001416.1| 9175 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:8:14:PASS
jpayne@0 60 gi|9626243|ref|NC_001416.1| 9234 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:12:10:0:1:PASS
jpayne@0 61 gi|9626243|ref|NC_001416.1| 9919 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:16:16:0:0:PASS
jpayne@0 62 gi|9626243|ref|NC_001416.1| 10127 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:13:12:0:1:PASS
jpayne@0 63 gi|9626243|ref|NC_001416.1| 10264 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:20:10:0:0:PASS
jpayne@0 64 gi|9626243|ref|NC_001416.1| 10421 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:7:9:0:0:PASS
jpayne@0 65 gi|9626243|ref|NC_001416.1| 10568 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:22:1:14:8:0:1:PASS
jpayne@0 66 gi|9626243|ref|NC_001416.1| 11066 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:12:11:0:1:PASS
jpayne@0 67 gi|9626243|ref|NC_001416.1| 11128 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:13:13:0:7:6:0:0:PASS
jpayne@0 68 gi|9626243|ref|NC_001416.1| 11782 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:15:7:0:0:PASS
jpayne@0 69 gi|9626243|ref|NC_001416.1| 12070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:16:2:7:9:2:0:PASS
jpayne@0 70 gi|9626243|ref|NC_001416.1| 12717 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:28:0:0:13:15:PASS
jpayne@0 71 gi|9626243|ref|NC_001416.1| 12795 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:17:10:PASS
jpayne@0 72 gi|9626243|ref|NC_001416.1| 12876 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:17:12:0:0:PASS
jpayne@0 73 gi|9626243|ref|NC_001416.1| 12959 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:14:8:PASS
jpayne@0 74 gi|9626243|ref|NC_001416.1| 12970 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:9:10:0:0:PASS
jpayne@0 75 gi|9626243|ref|NC_001416.1| 13107 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:7:10:0:1:PASS
jpayne@0 76 gi|9626243|ref|NC_001416.1| 13264 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:7:8:1:0:PASS
jpayne@0 77 gi|9626243|ref|NC_001416.1| 13542 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:13:12:0:0:PASS
jpayne@0 78 gi|9626243|ref|NC_001416.1| 13647 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:8:12:0:1:PASS
jpayne@0 79 gi|9626243|ref|NC_001416.1| 13952 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:9:17:0:0:PASS
jpayne@0 80 gi|9626243|ref|NC_001416.1| 13971 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:8:9:0:1:PASS
jpayne@0 81 gi|9626243|ref|NC_001416.1| 15384 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:17:7:1:0:PASS
jpayne@0 82 gi|9626243|ref|NC_001416.1| 15715 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:8:11:0:0:PASS
jpayne@0 83 gi|9626243|ref|NC_001416.1| 15967 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:10:10:0:10:0:0:0:PASS
jpayne@0 84 gi|9626243|ref|NC_001416.1| 16070 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:12:12:0:9:3:0:0:PASS
jpayne@0 85 gi|9626243|ref|NC_001416.1| 16654 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:15:9:PASS
jpayne@0 86 gi|9626243|ref|NC_001416.1| 16715 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:9:10:PASS
jpayne@0 87 gi|9626243|ref|NC_001416.1| 17142 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:10:7:0:0:PASS
jpayne@0 88 gi|9626243|ref|NC_001416.1| 17311 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:15:9:0:0:PASS
jpayne@0 89 gi|9626243|ref|NC_001416.1| 17854 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS
jpayne@0 90 gi|9626243|ref|NC_001416.1| 18151 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:9:9:0:0:PASS
jpayne@0 91 gi|9626243|ref|NC_001416.1| 18188 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS
jpayne@0 92 gi|9626243|ref|NC_001416.1| 18210 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:12:7:0:0:PASS
jpayne@0 93 gi|9626243|ref|NC_001416.1| 18420 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS
jpayne@0 94 gi|9626243|ref|NC_001416.1| 18598 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:14:11:PASS
jpayne@0 95 gi|9626243|ref|NC_001416.1| 18652 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:12:12:0:0:PASS
jpayne@0 96 gi|9626243|ref|NC_001416.1| 18989 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:32:0:12:20:0:0:PASS
jpayne@0 97 gi|9626243|ref|NC_001416.1| 19208 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:10:12:0:0:PASS
jpayne@0 98 gi|9626243|ref|NC_001416.1| 19448 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:17:17:0:7:10:0:0:PASS
jpayne@0 99 gi|9626243|ref|NC_001416.1| 19469 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:11:10:PASS
jpayne@0 100 gi|9626243|ref|NC_001416.1| 20079 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS
jpayne@0 101 gi|9626243|ref|NC_001416.1| 20099 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:14:14:PASS
jpayne@0 102 gi|9626243|ref|NC_001416.1| 20289 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:32:31:1:15:16:1:0:PASS
jpayne@0 103 gi|9626243|ref|NC_001416.1| 20367 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:9:20:0:0:PASS
jpayne@0 104 gi|9626243|ref|NC_001416.1| 21110 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:6:12:PASS
jpayne@0 105 gi|9626243|ref|NC_001416.1| 21320 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:12:14:0:0:PASS
jpayne@0 106 gi|9626243|ref|NC_001416.1| 21653 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:24:1:10:14:1:0:PASS
jpayne@0 107 gi|9626243|ref|NC_001416.1| 22220 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:10:11:0:0:PASS
jpayne@0 108 gi|9626243|ref|NC_001416.1| 22357 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS
jpayne@0 109 gi|9626243|ref|NC_001416.1| 22747 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:21:0:11:10:0:0:PASS
jpayne@0 110 gi|9626243|ref|NC_001416.1| 23362 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:14:0:14:0:0:5:9:PASS
jpayne@0 111 gi|9626243|ref|NC_001416.1| 23457 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:10:18:0:0:PASS
jpayne@0 112 gi|9626243|ref|NC_001416.1| 24043 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:25:1:11:14:1:0:PASS
jpayne@0 113 gi|9626243|ref|NC_001416.1| 24319 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS
jpayne@0 114 gi|9626243|ref|NC_001416.1| 24766 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:8:11:PASS
jpayne@0 115 gi|9626243|ref|NC_001416.1| 24930 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:10:10:1:0:PASS
jpayne@0 116 gi|9626243|ref|NC_001416.1| 25005 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:21:20:1:11:9:1:0:PASS
jpayne@0 117 gi|9626243|ref|NC_001416.1| 25158 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:10:11:1:0:PASS
jpayne@0 118 gi|9626243|ref|NC_001416.1| 25645 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:7:9:0:0:PASS
jpayne@0 119 gi|9626243|ref|NC_001416.1| 26173 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:18:1:8:10:1:0:PASS
jpayne@0 120 gi|9626243|ref|NC_001416.1| 26728 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:15:11:0:0:PASS
jpayne@0 121 gi|9626243|ref|NC_001416.1| 26972 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:20:6:0:0:PASS
jpayne@0 122 gi|9626243|ref|NC_001416.1| 27412 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:8:17:0:0:PASS
jpayne@0 123 gi|9626243|ref|NC_001416.1| 27539 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:16:13:0:0:PASS
jpayne@0 124 gi|9626243|ref|NC_001416.1| 27661 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:14:9:0:0:PASS
jpayne@0 125 gi|9626243|ref|NC_001416.1| 27722 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:9:16:0:0:PASS
jpayne@0 126 gi|9626243|ref|NC_001416.1| 27790 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19:0:0:8:11:PASS
jpayne@0 127 gi|9626243|ref|NC_001416.1| 27825 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS
jpayne@0 128 gi|9626243|ref|NC_001416.1| 27834 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:15:1:4:11:0:1:PASS
jpayne@0 129 gi|9626243|ref|NC_001416.1| 28045 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:24:2:15:9:0:2:PASS
jpayne@0 130 gi|9626243|ref|NC_001416.1| 28362 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:8:17:0:0:PASS
jpayne@0 131 gi|9626243|ref|NC_001416.1| 29265 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:13:11:0:0:PASS
jpayne@0 132 gi|9626243|ref|NC_001416.1| 29411 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:18:10:0:0:PASS
jpayne@0 133 gi|9626243|ref|NC_001416.1| 29435 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:33:33:0:16:17:0:0:PASS
jpayne@0 134 gi|9626243|ref|NC_001416.1| 29891 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:9:12:PASS
jpayne@0 135 gi|9626243|ref|NC_001416.1| 30125 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:20:20:0:11:9:0:0:PASS
jpayne@0 136 gi|9626243|ref|NC_001416.1| 30757 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:8:15:1:0:PASS
jpayne@0 137 gi|9626243|ref|NC_001416.1| 30890 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS
jpayne@0 138 gi|9626243|ref|NC_001416.1| 31328 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:14:1:7:7:0:1:PASS
jpayne@0 139 gi|9626243|ref|NC_001416.1| 31363 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS
jpayne@0 140 gi|9626243|ref|NC_001416.1| 31551 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:8:8:PASS
jpayne@0 141 gi|9626243|ref|NC_001416.1| 32086 . T A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:1:16:1:0:7:9:PASS
jpayne@0 142 gi|9626243|ref|NC_001416.1| 32660 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:14:10:0:0:PASS
jpayne@0 143 gi|9626243|ref|NC_001416.1| 33000 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:8:10:PASS
jpayne@0 144 gi|9626243|ref|NC_001416.1| 33591 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:30:0:30:0:0:16:14:PASS
jpayne@0 145 gi|9626243|ref|NC_001416.1| 33612 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:14:15:0:0:PASS
jpayne@0 146 gi|9626243|ref|NC_001416.1| 33865 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:25:25:0:12:13:0:0:PASS
jpayne@0 147 gi|9626243|ref|NC_001416.1| 34137 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:27:27:0:13:14:0:0:PASS
jpayne@0 148 gi|9626243|ref|NC_001416.1| 34370 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:22:0:0:10:12:PASS
jpayne@0 149 gi|9626243|ref|NC_001416.1| 34812 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:15:0:0:11:4:PASS
jpayne@0 150 gi|9626243|ref|NC_001416.1| 34920 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:9:7:PASS
jpayne@0 151 gi|9626243|ref|NC_001416.1| 35148 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:16:0:16:0:0:10:6:PASS
jpayne@0 152 gi|9626243|ref|NC_001416.1| 35802 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:19:19:0:5:14:0:0:PASS
jpayne@0 153 gi|9626243|ref|NC_001416.1| 35907 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:16:16:0:1:15:0:0:PASS
jpayne@0 154 gi|9626243|ref|NC_001416.1| 36010 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:9:0:9:0:0:0:9:PASS
jpayne@0 155 gi|9626243|ref|NC_001416.1| 36169 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:6:6:0:4:2:0:0:PASS
jpayne@0 156 gi|9626243|ref|NC_001416.1| 36642 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:15:15:0:2:13:0:0:PASS
jpayne@0 157 gi|9626243|ref|NC_001416.1| 37208 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:8:11:PASS
jpayne@0 158 gi|9626243|ref|NC_001416.1| 37387 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS
jpayne@0 159 gi|9626243|ref|NC_001416.1| 37519 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:20:2:8:12:2:0:PASS
jpayne@0 160 gi|9626243|ref|NC_001416.1| 37898 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:10:8:0:0:PASS
jpayne@0 161 gi|9626243|ref|NC_001416.1| 38073 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:11:11:0:0:PASS
jpayne@0 162 gi|9626243|ref|NC_001416.1| 38165 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:29:0:29:0:0:19:10:PASS
jpayne@0 163 gi|9626243|ref|NC_001416.1| 38575 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:14:13:1:7:6:1:0:PASS
jpayne@0 164 gi|9626243|ref|NC_001416.1| 39003 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:9:8:1:8:0:1:0:PASS
jpayne@0 165 gi|9626243|ref|NC_001416.1| 39206 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS
jpayne@0 166 gi|9626243|ref|NC_001416.1| 39484 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS
jpayne@0 167 gi|9626243|ref|NC_001416.1| 39485 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:10:10:PASS
jpayne@0 168 gi|9626243|ref|NC_001416.1| 40457 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:1:27:1:0:11:16:PASS
jpayne@0 169 gi|9626243|ref|NC_001416.1| 40835 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:18:0:11:7:0:0:PASS
jpayne@0 170 gi|9626243|ref|NC_001416.1| 40984 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:22:0:12:10:0:0:PASS
jpayne@0 171 gi|9626243|ref|NC_001416.1| 41064 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:26:26:0:14:12:0:0:PASS
jpayne@0 172 gi|9626243|ref|NC_001416.1| 41448 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:34:34:0:14:20:0:0:PASS
jpayne@0 173 gi|9626243|ref|NC_001416.1| 41954 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:13:10:0:0:PASS
jpayne@0 174 gi|9626243|ref|NC_001416.1| 42439 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:20:8:PASS
jpayne@0 175 gi|9626243|ref|NC_001416.1| 43306 . T G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:33:0:32:0:0:12:20:PASS
jpayne@0 176 gi|9626243|ref|NC_001416.1| 43470 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:23:1:12:11:0:1:PASS
jpayne@0 177 gi|9626243|ref|NC_001416.1| 44134 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:14:14:0:0:PASS
jpayne@0 178 gi|9626243|ref|NC_001416.1| 44201 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:28:28:0:12:16:0:0:PASS
jpayne@0 179 gi|9626243|ref|NC_001416.1| 44413 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:29:29:0:15:14:0:0:PASS
jpayne@0 180 gi|9626243|ref|NC_001416.1| 45364 . A . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:31:31:0:18:13:0:0:PASS
jpayne@0 181 gi|9626243|ref|NC_001416.1| 45409 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:30:30:0:19:11:0:0:PASS
jpayne@0 182 gi|9626243|ref|NC_001416.1| 46237 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:12:15:PASS
jpayne@0 183 gi|9626243|ref|NC_001416.1| 46283 . C . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:24:24:0:11:13:0:0:PASS
jpayne@0 184 gi|9626243|ref|NC_001416.1| 46842 . G . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:18:17:1:4:13:0:1:PASS
jpayne@0 185 gi|9626243|ref|NC_001416.1| 47425 . T . . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:23:23:0:12:11:0:0:PASS
jpayne@0 186 gi|9626243|ref|NC_001416.1| 47893 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:12:16:PASS