| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 53.7% | 27.9 / 65.7 | 54 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (19/6); new base A (0/29); total (19/35) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 9.64e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-07 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAT > NZ_CP009273/353514‑353688 | aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa > 1:1522890/1‑90 (MQ=255)aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa > 2:173597/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaa > 1:1652835/1‑90 (MQ=255) tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaa > 1:2731096/1‑90 (MQ=255) gCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccgc < 2:116089/90‑1 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccgc > 1:927234/1‑90 (MQ=255) aacaccCGCCCTTTTACCCACCGCCATGTAAAAAAACGCTTTCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGA‑AACAAAA‑CCGCCGt < 2:2499251/90‑1 (MQ=255) cacccGCGTTTTTACCCAACGCCTTGTGAAAAAATGCCTCCGGGGGGGGTGCCTCCCAGTTTTTTTTCCGCCGC‑AAAAAAA‑CCGCCGTtc < 2:2471827/87‑1 (MQ=255) cacccGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTtc < 2:1773700/87‑1 (MQ=19) cacccGCGCTTTTACCCACCCCCATGTGAAAAAATCCTTTCGGGGGGGTTGTCTGCCAGCTTTTTTCCCGCCGC‑AACAAAA‑CCGCCGTtc < 2:2368113/87‑1 (MQ=255) cacccGCGCTTTTACCCACCCCCATGTAAAAAAATCCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTtc < 2:927234/87‑1 (MQ=255) cacccGCGCTTTTACCCAACCCCATGTGAAAAAACCCCTTCGCGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGA‑AACAAAA‑CCGCCGTtc < 2:2537989/87‑1 (MQ=255) cacccGCGATTTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTtc < 2:294749/87‑1 (MQ=255) cacccGCCCTTTTACCCACCCCCATGTAAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTtc < 2:276545/87‑1 (MQ=16) aacccGCCCTTTTACCCACCCCCTTGTGAAAAAATGCCTTCGCGGGGGCTGTCCGCCAGCTTTTTTCCCCCCGC‑AAAAAAA‑CCGCCGTtc < 2:1956253/87‑1 (MQ=16) acCGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AACAAAA‑CCGCCGTtctc < 2:725347/90‑1 (MQ=25) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTcc > 2:1251823/1‑90 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTcc > 2:2235848/1‑90 (MQ=255) aTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCagta > 1:2471827/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:25773/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1411063/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:2124402/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:395713/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:1827804/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:2268754/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:2398822/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:2005259/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:917282/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGGGGCggtt > 1:1692273/1‑88 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGGGGCgggg > 1:2588071/1‑90 (MQ=255) gaaaaaaTGCCTTCGCGGCGGCTTTCGGCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa < 2:1029865/88‑1 (MQ=255) aaaaatTGCTTTCGGGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:2134387/89‑1 (MQ=255) aaaaatTCCCTCCGCGGGGGCTGCCTCCCATTTTTTTCCCCGCCAC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 1:2124402/89‑1 (MQ=255) aaaaaaTGCCTCCGGGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:91198/89‑1 (MQ=255) aaaaaaTGCCTCCGCGGGGGCTGTCTGCCATTTTTTTTCCCCCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:2596039/89‑1 (MQ=255) aaaaaaTCCCTTCGGGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:1005947/89‑1 (MQ=255) aaaaaaTCCCTCCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt < 2:917282/89‑1 (MQ=255) aaaaaTCCCTTCGCGGGGGTTGTCTGCCATTTTTTTTCCCCCCGA‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:1168670/90‑1 (MQ=255) gCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAGAtttt > 2:1806088/1‑89 (MQ=255) tCGGGGGGGCTGTCTGCCAGTTTTTTTCCCCCCCC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:2129805/90‑1 (MQ=255) ccggggcggcTTTCGCCCAGTTTTTTTCCCGCCCA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:892576/86‑1 (MQ=255) ggggggcTGTCTGCCAGTTTTTTTCCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt < 2:1411063/86‑1 (MQ=255) gcggcTTTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 2:573381/90‑1 (MQ=255) gcggcTGCCCCCCGGCTTTTTTCCCCCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa < 2:2899524/90‑1 (MQ=255) tttttttcCCGCCGA‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:1149235/87‑1 (MQ=255) cttttttcCCTCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:1692273/87‑1 (MQ=255) tttttcCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:130789/89‑1 (MQ=255) tttttcCCGCCAC‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1920904/89‑1 (MQ=255) tttttcCCGCCAA‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:2848873/89‑1 (MQ=255) tttttcCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:25773/89‑1 (MQ=255) tttttcCCCCCCC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:508855/89‑1 (MQ=255) tttttCCCCCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:312598/90‑1 (MQ=255) tttttCCCCCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 2:1671322/90‑1 (MQ=255) tttttCCCCCCA‑AAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:1806088/90‑1 (MQ=255) tttcCCGCCAA‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:173597/90‑1 (MQ=255) cgccgc‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAACTTTTAAACCCCCCTTTTGTGTGGGGATCGGTTCTGGt > 2:2457815/1‑90 (MQ=255) aacaaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt < 2:2403202/90‑1 (MQ=255) aacaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt < 1:2530862/90‑1 (MQ=255) | ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAT > NZ_CP009273/353514‑353688 |
| 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: ‑ |