| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 6,967 | 0 | C | T | 20.0% | 87.8 / 12.6 | 57 | Q25* (CAG→TAG) | r1tp11 | ORF11 |
| Reads supporting (aligned to +/- strand): ref base C (44/0); new base T (11/0); total (57/0) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TCGTGGCACAAAGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGTAAGAAT > NC_004302/6893‑7040 | gagTGGCACAAAGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAacac > 1:9721108/3‑75 (MQ=255) atactcacaAAGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTTGGAGACTTCCTCTTGAAacac > 1:5383073/6‑75 (MQ=255) agtaacacaAAGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAAcaca > 1:16058245/6‑75 (MQ=255) gctcacaAAGAAGAATGATAGATAAACGAACTATTCAAACACAAAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAg > 1:3559583/4‑75 (MQ=255) gtcaaaaGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAA‑ACAGGCta > 1:11780386/5‑74 (MQ=255) gacgtggaaggaTGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCtt > 1:15922396/7‑75 (MQ=255) ttgggttGATAGATAAACGAACTATTCAAACAC‑AAAGA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAt‑t > 1:3580712/7‑75 (MQ=255) ctataaTGATAGATAAACGAACTATTCAAACAC‑‑AAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAt‑tt > 1:11809085/5‑75 (MQ=255) cgggctggatagataAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAt‑t > 1:12068686/8‑75 (MQ=255) atttaaTGAT‑GATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAt‑tt > 1:15545669/5‑75 (MQ=255) gccagaatagataAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTc > 1:8567104/7‑75 (MQ=255) atagagataga‑aaACGAACT‑TTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCa > 1:8343130/6‑75 (MQ=255) ggagataAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCtt > 1:1254337/3‑75 (MQ=255) tgatgataCTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTatgct > 1:10424371/8‑75 (MQ=255) gAACTATTCAAACAC‑AAAAATTTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTatgctgaat > 1:2317579/1‑75 (MQ=255) gAACTATTCAAACAC‑AAAAATTTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTatgctgaat > 1:6298588/1‑75 (MQ=255) aTTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgat > 1:11279251/1‑75 (MQ=255) agaaaaCAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatg > 1:4894713/4‑75 (MQ=255) cgagtcac‑aAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatga > 1:16776775/6‑75 (MQ=255) tatacaaaaaa‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatgatg > 1:2614906/7‑75 (MQ=255) tatacaaaaaa‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatgatg > 1:15620413/7‑75 (MQ=255) agtac‑aAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatgatga > 1:3103215/4‑75 (MQ=255) taaacggaaa‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCtgatgatga > 1:16724841/8‑75 (MQ=255) agttta‑TTTTA‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGa > 1:11362891/6‑75 (MQ=255) agattaagagaCTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTg > 1:12329925/8‑75 (MQ=255) cggcggggaCTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGATGATGATGATGGAGTTGTa > 1:4233328/8‑75 (MQ=255) gatatagttCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGaa > 1:13793757/8‑75 (MQ=255) attttgttCCTCTTGAAACACAGGCTTAGTAT‑TTCCATCTTATGCTAAATGCTGATGATGATGGAGTTGTAGAAg > 1:524014/7‑75 (MQ=255) aaaCTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑t > 1:11684732/3‑75 (MQ=255) ttattcagAAACA‑AGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTccc > 1:2645279/8‑75 (MQ=255) ttatattGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcc > 1:9732894/6‑75 (MQ=255) tgtgtgggAAATACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcc > 1:17092589/8‑75 (MQ=255) gatcggtGAATCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcc > 1:9381574/7‑75 (MQ=255) gaactctGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcc > 1:9574596/7‑75 (MQ=255) tgactTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTccc > 1:15699231/4‑75 (MQ=255) tgaccgtaaaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTccc > 1:6621165/8‑75 (MQ=255) tcggaagaaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:9007590/8‑75 (MQ=255) gagaagAAACATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcccc > 1:10352088/6‑74 (MQ=255) gagaagAAACATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTcccc > 1:4151620/6‑74 (MQ=255) ctgtaagaaCAGAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:14439710/8‑75 (MQ=255) ctgcaataaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:1743714/8‑75 (MQ=255) cgcagataaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:5721810/8‑75 (MQ=255) cgcagataaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:4318448/8‑75 (MQ=255) caggataaaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:10686120/7‑75 (MQ=255) caggataaaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:12562163/7‑75 (MQ=255) aaagtGAAATACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCg > 1:9281891/5‑75 (MQ=255) cgatGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:12823729/4‑75 (MQ=255) cgatGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:12843776/4‑75 (MQ=255) tttGAAAAATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGtt > 1:1642181/2‑75 (MQ=255) tgcagaaCATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGCTTTTTCCCGt > 1:7041650/6‑75 (MQ=255) tgaataaCATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGtt > 1:12696352/6‑75 (MQ=255) cggaaaaCATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGtt > 1:8285447/5‑75 (MQ=255) catgcaaCATAGGCTTTGTATATTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:14151197/6‑75 (MQ=255) catgcaaCATAGGCTTTGTATATTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:12381211/6‑75 (MQ=255) catgcaaCATAGGCTTTGTATATTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:16266298/6‑75 (MQ=255) catgcaaCATAGGCTTTGTATATTCCATCTTATGATGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGt > 1:14139417/6‑75 (MQ=255) atgtgaaCATAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGtt > 1:13616164/6‑75 (MQ=255) tcctaaCACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCggtt > 1:4028619/5‑72 (MQ=255) gggtaggacaGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTg > 1:5905524/8‑75 (MQ=255) gctgtagacaGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGT‑TTTTCCCGTTg > 1:12755221/8‑75 (MQ=255) ctGAAACTCA‑GCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGt > 1:16649529/2‑75 (MQ=255) agggaaCACTGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTg > 1:1519441/5‑75 (MQ=255) ttgggtccaGGGTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGt > 1:1659378/8‑75 (MQ=255) ggggatacaGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGt > 1:15298703/7‑75 (MQ=255) gaacacacAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGCTTTTTCCCGTTg > 1:1307233/5‑75 (MQ=255) ccaacaGGCATCGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGTAAg > 1:262578/4‑75 (MQ=255) agacaGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGTAAGa > 1:8548067/3‑75 (MQ=255) agacaGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGTAAGa > 1:1744469/3‑75 (MQ=255) caGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGCTTTTTCCCGTTGTAAGAAt > 1:3640508/1‑75 (MQ=255) | TCGTGGCACAAAGAAGAATGATAGATAAACGAACTATTCAAACAC‑AAAAA‑TTTTT‑GAGACTTCCTCTTGAAACACAGGCTTTGTAT‑TTCCATCTTATGCTGAATGCTGATGATGATGGAGTTGTAGAAGC‑TTTTCCCGTTGTAAGAAT > NC_004302/6893‑7040 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |