| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 54.8% | 25.9 / 77.8 | 62 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (21/7); new base A (1/33); total (22/40) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.18e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.56e-04 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAA > NZ_CP009273/353515‑353687 | tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa > 2:1321712/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:674060/1‑90 (MQ=255) aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGt > 1:317947/1‑90 (MQ=255) cacccGCGTTTTTACCCACCGCCATGTGAAAAAATGCC‑TTC‑GGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:1106696/87‑1 (MQ=18) cacccGCGCTTTTACCCACCGCCATGTGAAAAAATGCC‑TTC‑GCGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:1003054/87‑1 (MQ=21) cacccGCGCTTTTACCCACCGCCATGTGAAAAAATCCC‑TTC‑GCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:338644/87‑1 (MQ=21) cacccGCGCTTTTACCCACCCCCATGTCAAAAAATCCC‑TCC‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAACAAAA‑CCGCCGTtc < 1:1321712/87‑1 (MQ=19) cacccGCGCTTTTACCCAACGCCAGGTGAAAAAATGCT‑TCC‑GCGGGGGCTGTCTCCCACTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 1:1258468/87‑1 (MQ=255) cacccGCGCTTTTACCCAACCCCATGTGAAAAAATGCC‑TTC‑GCGGCGGCTTTCTCCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTtc < 1:981640/87‑1 (MQ=16) cacccGCGCATTTATCCACCGCCATGTGCAAAAATGCC‑TTC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:107961/87‑1 (MQ=21) cacccGCGCATTTACCCACCCCCATGTGAAAAAATGCC‑TTC‑GGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 1:609776/87‑1 (MQ=21) cacccGCGCATTTACCCAACGCCATGTGAAAAAATGCC‑TTC‑GCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc < 1:1279174/87‑1 (MQ=21) cacccGCCCATTTACCCAACCCCTTGTGAAAAAATGCC‑TCC‑GCGGCGGCTGTCTGCCAGCTAATTTTCCGCCGCAACAAAA‑CCGCCGTtc < 1:609727/87‑1 (MQ=25) caacCGCGCTTTTCCCCACCCCCATGTAAAAAAATGCC‑TTC‑GCGGCGGTTTTCTGCCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:676825/90‑1 (MQ=16) agcccGCGCTTTTACCCACCCCCATGTGAAAAAATGCC‑TCC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:431170/87‑1 (MQ=19) ccGCGCTTTTACCCACCCCCATGTGAAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtctct < 1:392862/90‑1 (MQ=21) gcgcATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc > 2:1167636/1‑90 (MQ=255) gcgcATTTACCCACCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGTTTTCGCCAAGCTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTcc < 1:32817/90‑1 (MQ=21) tATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtagct > 2:431170/1‑88 (MQ=255) tATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg > 1:568259/1‑90 (MQ=255) tATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg > 1:668002/1‑90 (MQ=255) tATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGGCTGCCAGCTATTTTTCCGCCGCAAAAAAA‑CCGCCGTTCTTTCCAATAGTg > 2:913298/1‑90 (MQ=25) aTCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtagctg > 1:1084770/1‑87 (MQ=255) cAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgg > 1:378902/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1328338/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:153820/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:436404/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:326281/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1244953/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:295071/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1310314/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:801036/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggcg > 2:524451/1‑88 (MQ=255) gCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggg > 2:613056/1‑88 (MQ=255) cccATGTGCAAAAATCCC‑TCC‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 1:230331/89‑1 (MQ=37) cccATGTAAAAAAATCCC‑TCC‑GCGGCGGCTGTCGGCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGGGGGGCa < 1:958626/89‑1 (MQ=255) gaaaaaaaaTCCC‑CCC‑GGGGCGTTTCTCTGCCACTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga < 2:1086158/86‑1 (MQ=255) aaaaaaTGCC‑TCC‑GGGGGGGCTGTCGCCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:1202120/89‑1 (MQ=255) aaaaaaTGCC‑TCC‑GCGGGGGTTGCCGGCCGTTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:826072/89‑1 (MQ=255) aaaaaaTGCC‑TCC‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:351031/89‑1 (MQ=38) aaaaaTTCCTTTC‑GGGGGGGCTGTCGGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:483559/90‑1 (MQ=255) aaaaaTGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:198271/90‑1 (MQ=255) aaaaaTGCC‑TCC‑GGGGCGGTTTTCGGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:316184/90‑1 (MQ=255) aaaaaTCCC‑TCC‑GGGGCGTTTGTCGGCCAGTTTTTTTCCCGCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 2:204367/90‑1 (MQ=255) aaaaTGCC‑CTCGGGGGGGGTTGCCTCCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:647616/90‑1 (MQ=255) gCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGGtttt > 1:916849/1‑89 (MQ=255) c‑TTC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg < 1:518326/90‑1 (MQ=255) ccggggcggcTTTCGGCCAGTTTTTTTGGCCCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:505587/86‑1 (MQ=255) gcggcTGTCTGCATGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 1:247529/90‑1 (MQ=255) gcggcTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 1:476700/90‑1 (MQ=255) gttGTCCGCCAGTTTTTTTCCCCCCCAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt < 1:224851/88‑1 (MQ=255) gcTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt < 1:54955/90‑1 (MQ=255) tcccccAGTTTTTTTCCCGCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg < 1:581748/86‑1 (MQ=255) tttttcCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:664329/89‑1 (MQ=255) tttttcCCGCCACAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:610531/89‑1 (MQ=255) tttttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:425647/89‑1 (MQ=255) tttttCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1112938/90‑1 (MQ=255) tttcCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:339108/90‑1 (MQ=255) ttccccgccaAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:555963/86‑1 (MQ=255) tcccgccgCAACAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct < 1:1078899/88‑1 (MQ=255) tCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAACTTTTAACCCCCCCTGTTTTGTGGGGAACGctggtg > 1:278264/1‑90 (MQ=255) cccgaAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 1:667173/89‑1 (MQ=255) cacaacaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc < 1:899590/88‑1 (MQ=255) aaacaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa < 1:1328832/89‑1 (MQ=255) | TTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAA > NZ_CP009273/353515‑353687 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |