| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 54.2% | 39.4 / 98.9 | 72 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (24/9); new base A (0/39); total (24/48) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.85e-12 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.26e-07 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353515‑353689 | tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACaaa > 2:201721/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:1050918/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:374234/1‑90 (MQ=255) cccAACACCCGCGCATTTACCCACCCCCATGTGCAAAAATGCCTTCGGGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑ccgc < 2:1398016/89‑1 (MQ=18) aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGt > 1:1510351/1‑90 (MQ=255) aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGt > 2:412571/1‑90 (MQ=255) cacccGCGTTTTTATCCAACGCCATGTGAAAAAATGCTTTCGGGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:1536116/87‑1 (MQ=21) cacccGCGCTTTTCCCCACCCCCATGTGAAAAAATGCTTCCGGGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:1500902/87‑1 (MQ=16) cacccGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTTCGGGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:315297/87‑1 (MQ=21) cacccGCGCATTTACCCACCCCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:485970/87‑1 (MQ=21) cacccGCGCATTTACCCAACGCCATGTGAAAAAATGCCTTCGGGGGGGCTGTCTG‑CCAGCTATTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:428226/87‑1 (MQ=25) cacccGCGCATTTACCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:736293/87‑1 (MQ=21) cacccGCGCATTTACCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:242019/87‑1 (MQ=25) cacccGCGCATTTACCCAACCCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:495391/87‑1 (MQ=21) cacccGCCCTTTTACCCACCCCCATGTCCAAAAAGCCCTTCGCGGGGGTTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:1440128/87‑1 (MQ=255) cacccGCCCTTTTACCCACCCCCATGTAAAAAAACGCCTCCGGGGGGGCTGTCGG‑CCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:1537778/87‑1 (MQ=255) cacccGCACTTTTACCAAACCCCATGTAAAAAAAGCCCTCCGCGGCGGTTGTCTC‑CCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:1856702/87‑1 (MQ=255) caacCGCGCATTTACCCACCGCCATGTAAAAAAATCCCTCCGCGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:1437928/90‑1 (MQ=21) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc > 2:1653567/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc > 1:72320/1‑90 (MQ=255) tATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg > 1:667024/1‑90 (MQ=255) cccACCGCCTTGTGAAAAAATGCTTCGGGGGGGGCTGTCTG‑CCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 2:402309/89‑1 (MQ=255) cccACCGCCATGTGAAAAATTCCCTTCGCGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 2:563682/89‑1 (MQ=25) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg < 1:886223/69‑1 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑cccccg > 2:886223/1‑69 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:604127/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1593260/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1206596/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:741729/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:803942/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:686628/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:724591/1‑90 (MQ=255) cccATGTGAAAAAATGCCTCCGGGGCGGCTGTCTG‑CCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 2:281471/89‑1 (MQ=37) cATGTAAAAAACTCCCTTCGGGGGGGCTGTCTG‑CAATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAag < 2:851077/90‑1 (MQ=255) aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAaga > 2:1190617/1‑90 (MQ=255) aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAaga > 2:1695431/1‑90 (MQ=255) aaaaaaaTCCCTCGGGGGCGGTTTTCTG‑CCGTTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaaa < 1:763022/88‑1 (MQ=255) aaaaaaTGCTTCCGGGGGGGTTGTCTG‑CCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAt < 2:1510351/89‑1 (MQ=255) aaaaaTGCTTCCGCGGGGGTTGTCTC‑CCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATa < 2:1658534/90‑1 (MQ=255) aaaaaTGCCTTTGGGGGGGTTTTCGCCCCAGTTTTTTTCCCCCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAt < 1:585235/90‑1 (MQ=255) aaaTGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGACGA‑Ggaaaaaa > 1:1747293/1‑86 (MQ=38) ccggggcggtTGTCCC‑CCATTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGcc < 2:1323485/86‑1 (MQ=255) ccggggcggcTGTCTG‑CCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGcc < 2:511845/86‑1 (MQ=255) ccgcgGCGGCTGTCTC‑CCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGcc < 2:1691112/89‑1 (MQ=255) gggcgccTGTCTC‑CCATTTTTTTTCCCCCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGt < 1:847630/89‑1 (MQ=255) ggggcTGTCTG‑CCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCa < 2:456396/88‑1 (MQ=255) gcggcTTTCTG‑CCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCa < 2:593424/90‑1 (MQ=255) gttGTCCG‑CCAGTTTTTTTCCCCCCCCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgt < 2:1294855/88‑1 (MQ=255) gcTGTCTC‑CCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgt < 2:289988/90‑1 (MQ=255) g‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtc > 1:644791/1‑36 (MQ=255) g‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtc < 2:644791/36‑1 (MQ=255) tttttttcCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:1278619/87‑1 (MQ=255) tttttcCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1210641/89‑1 (MQ=255) tttttcCCGCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:657089/89‑1 (MQ=255) tttttcCCGCAACAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1459943/89‑1 (MQ=255) tttttcCCCCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:382352/89‑1 (MQ=255) tttttcCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:40410/89‑1 (MQ=255) tttttcCCCCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:657101/89‑1 (MQ=255) tttttCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1030152/90‑1 (MQ=255) ttttcCCCCCCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1027539/90‑1 (MQ=255) tttcCCGCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:1160422/90‑1 (MQ=255) tttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:978433/90‑1 (MQ=255) ttcccgccgCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc < 2:684476/87‑1 (MQ=255) tcccgccgAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 2:526748/88‑1 (MQ=255) cgccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc > 1:942620/1‑36 (MQ=255) cgccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 2:942620/36‑1 (MQ=255) cgccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc > 1:1656728/1‑36 (MQ=255) cgccgcAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 2:1656728/36‑1 (MQ=255) gccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAAATTTTAACCCCTCCTGTTTTGGGGGGATCGCTGCTgggt > 2:336369/1‑88 (MQ=255) gccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGGAAAAAATTTTAAACCC‑TCCTGTTGTTTGGGGAACGCTGCTgggg > 2:773900/1‑88 (MQ=255) gccgaAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:156304/90‑1 (MQ=255) cccccaaaaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 2:641814/86‑1 (MQ=255) ccgcAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa < 1:369692/90‑1 (MQ=255) caaaaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa < 1:1314875/90‑1 (MQ=255) acaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg < 2:134471/90‑1 (MQ=255) acaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg < 2:714347/90‑1 (MQ=255) | TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353515‑353689 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |