| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 57.1% | 17.6 / 44.4 | 35 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (13/2); new base A (0/20); total (13/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.11e-08 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.49e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC > NZ_CP009273/353514‑353675 | aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa > 1:18909/1‑90 (MQ=255) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc > 1:250887/1‑90 (MQ=255) aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGt > 1:443762/1‑90 (MQ=255) cacccGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTT‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAACAAAA‑CCGCCGTtc < 1:626211/87‑1 (MQ=21) cacccGCGCTTTTACCCAACGCCATGTAAAAAAATGCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:815153/87‑1 (MQ=21) cacccGCCCTTTTACCCACCCCCTTGTGAAAAAATCCCTC‑CGCGGCGGCTGTCCGCCACTTATTTTCCCGCCGCAAAAAAA‑CCGCCGTtc < 1:136490/87‑1 (MQ=255) caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtc > 2:9925/1‑90 (MQ=255) ccGCGCTTTTACCCACCCCCATGTAAAAAAATCCCTC‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTtctct < 1:622410/90‑1 (MQ=255) gcgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc > 2:136490/1‑90 (MQ=255) cgcATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCa > 2:381736/1‑90 (MQ=255) tATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg > 2:622410/1‑90 (MQ=255) tCCACCGCTATGAGAAAAAATCCCTT‑CGCGGGGCCTCCCCCCCCGTTTTTTCCCCGCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGc < 2:667994/90‑1 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:843432/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:387843/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:347061/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:286254/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGCTCTCTCCAGTAGTGGCgggg > 2:622806/1‑90 (MQ=255) aaaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:347061/90‑1 (MQ=38) aaaaaTGCCTC‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:9925/90‑1 (MQ=38) aaaaaTCCCTC‑CGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:253897/90‑1 (MQ=255) aaaaTTCCTTCCGGGGCGGCTTTTTGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa < 1:577812/90‑1 (MQ=255) gCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAGATTTa > 1:25682/1‑90 (MQ=255) ctcggcggcgCTTTTCTCCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg < 1:473470/86‑1 (MQ=255) ctccgcgGGGGCTGTCGGCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg < 1:182743/87‑1 (MQ=255) t‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:381736/90‑1 (MQ=255) t‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:53539/90‑1 (MQ=255) ccggggcggcTGTCGGCCATTTTTTTCCCCGCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:645693/86‑1 (MQ=255) ccggggcggcTGTCGCCCAGTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 1:286254/86‑1 (MQ=255) ccgcgGGGGCTGTCTGCCATTTTTTTCCCCGCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc < 2:367487/89‑1 (MQ=255) tcgCCAGCTTTTTTCCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg < 2:18909/88‑1 (MQ=255) tttttttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:50415/87‑1 (MQ=255) cttttttcCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 1:67467/87‑1 (MQ=255) tttttcCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:701288/89‑1 (MQ=255) tttttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:622806/89‑1 (MQ=255) gccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc > 2:125583/1‑35 (MQ=255) gccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc < 1:125583/35‑1 (MQ=255) | ATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC > NZ_CP009273/353514‑353675 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |