| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 55.0% | 37.0 / 101.6 | 80 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (25/11); new base A (0/44); total (25/55) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.65e-12 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.71e-08 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353517‑353689 | tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑c > 1:1015637/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:600302/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:1478262/1‑90 (MQ=255) cccAACACCCGCGCTTTTACCCAACCCCATGTGAAAAAATCCCTT‑CGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAACAAAA‑ccgc < 2:1478262/89‑1 (MQ=255) caacaaCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ctgccg < 2:1556854/90‑1 (MQ=255) aacaccCGCGCATTTACCAACCCCCGTGTACAAAAATCCCTC‑CGGGGGGGCTTTCTGCCAGCTATTTTCCCGCCCCAAAAAAA‑CCGCCGt < 2:814287/90‑1 (MQ=255) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGtt > 2:873955/1‑90 (MQ=255) acaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGtt > 2:411555/1‑90 (MQ=255) cacccGCGCTTTTACCCACCCCCATGTAAAAAAATGCTTC‑CGGGGCGGCTGTCCCCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:891519/87‑1 (MQ=255) cacccGCGCTTTTACCCAACGCCATGGGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:370238/87‑1 (MQ=21) cacccGCGCTTTTACCAACCGCTTTGTGCAAAAACGCCTT‑CGCGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGAAACAAAA‑CCGCCGTtc < 2:715826/87‑1 (MQ=255) cacccGCGCATTTACCCACCCCCATGTGCAAAAATCCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 2:83418/87‑1 (MQ=25) cacccGCGATTTTACCCACCCCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:258456/87‑1 (MQ=21) cacccGCCCTTTTACCCAACCCCATGTGAAAAAATCCCTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTtc < 2:132556/87‑1 (MQ=16) caacCGCGCATTTACCCACCCCCTTGTAAAAAAATCCCTT‑CGGGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 2:1041254/90‑1 (MQ=255) aacccGCGCTTTTATCCACCCCCATGTGAAAAAATGCCTT‑CGGGGGGGTTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAA‑CCGCCGTtc < 2:846120/87‑1 (MQ=21) ccGCGCTTTTACCCACCCCCTTGTGAAAAAATCCCTT‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtctct < 2:845211/90‑1 (MQ=255) ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctct > 1:123850/1‑90 (MQ=255) cgcgCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctctc > 1:1041194/1‑90 (MQ=255) gcgcTTTCACCCACCCCCATGTGAAAAAATGCCTC‑CGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTcc < 2:1095184/90‑1 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc > 1:1442568/1‑90 (MQ=255) cgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCa > 2:912578/1‑90 (MQ=255) cgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCa > 2:1053334/1‑90 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtag > 1:715826/1‑90 (MQ=255) tttACCCACCCCCTTGTCAAAAAAGCCCTC‑CCCGGCGGCTGCCCGCCACTTTTTTTCCCCCCGCAACAAAA‑CCGCCGTTCTCTCCagtag < 2:1269231/90‑1 (MQ=255) tATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg > 2:1265342/1‑90 (MQ=255) aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtagctg > 2:933077/1‑87 (MQ=255) aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTgg > 1:1221785/1‑90 (MQ=255) cccACCGCCATGTGAAAAAATGCCTG‑CGGGGGGGCTGTCTGCCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 2:892776/89‑1 (MQ=255) ccACCGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCg < 2:137166/90‑1 (MQ=25) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1162440/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:422331/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:272636/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:313495/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:847042/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1558315/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1200853/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1446076/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1226581/1‑90 (MQ=255) cccATGTCCAAAAATCCTTT‑CGGGGGGGCTTTCTGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 2:382767/89‑1 (MQ=255) ccttgtcCAAAAAGCCCTC‑CGCGGCGGTTTCCGGCCCGCTTTTTTTCCCCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCaa < 2:468427/87‑1 (MQ=255) aaaaaaaTGCTTC‑CGGGGGGGCTGTCTCCCCCCTTTTTTCCCCCCGCAACAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa < 2:984943/88‑1 (MQ=255) aaaaaaGGCCTC‑CGGGGGGGTTGTCTCCCACTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:769991/89‑1 (MQ=255) aaaaaaCCCCTC‑CGGGGCGGTTTTCTGCCGGTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:422331/89‑1 (MQ=255) aaaatTGCCTC‑CGGGGCGGCTGTCGGCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:411555/90‑1 (MQ=255) aaaaaTGCCTTCCGCGGGGGTTGTCTCCAATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:316660/90‑1 (MQ=255) aaaaaTCCCTT‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:313495/90‑1 (MQ=255) aaaaaTCCCTC‑CGCGGCGGTTCCCTGCCTGCTTTTTTCCCGCGGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:939821/90‑1 (MQ=255) aaaaTTCCTTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:161177/90‑1 (MQ=255) ccTC‑CGGGGCGGCTGCCTCCAATTTTTTTTCCCCCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa < 1:1131150/90‑1 (MQ=255) cttccgcgGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa < 2:1106269/86‑1 (MQ=255) t‑CGGGGGGGTTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:591015/90‑1 (MQ=255) t‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:261331/90‑1 (MQ=255) ccggggcggtTGCCTGCAAGCTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:13626/86‑1 (MQ=255) ccgcgGGGGCTGTCCGCCAGTTTTTTTCCCCCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:1149444/89‑1 (MQ=255) cggcggCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt < 2:456079/90‑1 (MQ=255) gcggcTGTCTGCCACTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 2:248935/90‑1 (MQ=255) gcggcTGTCGGCCATCTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 1:1232925/90‑1 (MQ=255) gttGTCGGCCGGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt < 2:1427394/88‑1 (MQ=255) tCTGCCACCTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg < 2:1307756/90‑1 (MQ=255) gCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGAGAAAAAAAATTAAGACCCCCCTGTTGTTTgg > 1:214444/1‑90 (MQ=255) tttttttcCCGCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:652072/87‑1 (MQ=255) tttttttCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:1226581/88‑1 (MQ=255) tttttttCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:86734/88‑1 (MQ=255) tttttcCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:605450/89‑1 (MQ=255) tttttcCCGCCCAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:435443/89‑1 (MQ=255) tttttCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:730068/90‑1 (MQ=255) tttttCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1388951/90‑1 (MQ=255) tttttCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:584215/90‑1 (MQ=255) ttttcCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1175987/90‑1 (MQ=255) tttcCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:991115/90‑1 (MQ=255) tttcCCGCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:1506630/90‑1 (MQ=255) tttcCCCCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:38785/90‑1 (MQ=255) tttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:426285/90‑1 (MQ=255) ttccccgccgCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:1491452/86‑1 (MQ=255) tcccgccgCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 2:272636/88‑1 (MQ=255) tcccgccgCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 2:552704/88‑1 (MQ=255) tcccgccaCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 1:33964/88‑1 (MQ=255) cccgccgAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg < 1:294292/89‑1 (MQ=255) gccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAAACCCCCCTTTTGTGTGGGGAACGCTGCTggga > 2:411878/1‑88 (MQ=255) ccacaaaaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa < 2:1571145/87‑1 (MQ=255) aaacaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa < 2:1508356/89‑1 (MQ=255) aacaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt < 1:1453391/90‑1 (MQ=255) acaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg < 1:33558/90‑1 (MQ=255) | TCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATG > NZ_CP009273/353517‑353689 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |