| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 60.0% | 4.6 / 47.6 | 40 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (14/2); new base A (0/24); total (14/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.17e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.14e-04 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTA > NZ_CP009273/353516‑353683 | ttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa‑a > 1:110299/1‑90 (MQ=255) cacccGCGCTTTTATCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAACAAA‑A‑CCGCCGTtc < 2:998649/87‑1 (MQ=25) cacccGCGCTTTTACCCACCGCCTTGTGAAAAAATGCCTTCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTtc < 2:493961/87‑1 (MQ=21) cacccGCGCATTTACCCAACCCCATGTAAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAA‑A‑CCGCCGTtc < 2:1229422/87‑1 (MQ=21) aacccGCGATTTTACCCACCCCCTTGTCAAAAAATCCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTtc < 2:743821/87‑1 (MQ=255) acccGCGCTTTTACCCACCCCAATGTAAAAAAATGCTTTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTtct < 2:1264379/88‑1 (MQ=255) ccGCGCTTTTACCCACCCCCTTGTGAAAAAATGCTTTGGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTtctct < 2:67043/90‑1 (MQ=255) ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTtctct > 2:404026/1‑90 (MQ=255) cgcgCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTtctctc > 2:419172/1‑90 (MQ=255) gcgcTTTTACCAACCCCCATGTGAAAAAATGCTTTCGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTcc < 2:110299/90‑1 (MQ=255) tttATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGCCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCagtag > 2:1470025/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGctgtc > 2:671444/1‑86 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:1103264/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:973004/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 1:572527/1‑90 (MQ=255) aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCgggg > 2:750295/1‑90 (MQ=255) gCCATGTAAAAAAATCCCTGCGGGGGGGTTGTCGGCCGGTTTTTTTCCCGCCAAAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 1:1007129/90‑1 (MQ=255) cccATGTAAAAAAATCCCTCGGCGGCGGTTTTCGGCAAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 1:450665/89‑1 (MQ=255) aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCTCCGTTCTCTCCAGTAGTGGCGGGACagaa > 2:1406193/1‑87 (MQ=37) aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAagg > 2:43869/1‑89 (MQ=255) aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGagt > 1:1461851/1‑89 (MQ=255) cAAAAATCCTTCCGGGGGGGTTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAt < 2:1527771/90‑1 (MQ=255) aaaacTGCCTCCGCGGCGCCTGCCCCCCGTTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa < 2:239473/90‑1 (MQ=255) aaaacTCCCTCCGGGGCGGTTTTCCGCCGCCTTTTTTCCCCCCAAAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa < 2:1372790/90‑1 (MQ=255) aaaaaTCCCTTCGCGGCGGCTGTCTGCCATTTTTTTTCCCCCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa < 2:934920/90‑1 (MQ=255) tGCCTCCGGGGCGGCTGTCCCCCCCTTTTTTTCCCCCCGAAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCttt < 2:369631/90‑1 (MQ=255) cgggggcggcTGTCGCCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGcc < 2:1302522/86‑1 (MQ=255) cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGAG‑AAAAAAGTTTaaagcc > 2:35760/1‑86 (MQ=255) gggcggcTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt < 2:9759/89‑1 (MQ=255) ggggcTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AGATAGCTTTAAGCCCGTCa < 2:115357/88‑1 (MQ=255) gcggcTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCa < 2:637516/90‑1 (MQ=255) cttttttCCCCCCAAAAAAA‑ACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc < 2:979601/88‑1 (MQ=255) tttttcCCGCCCAAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:113433/89‑1 (MQ=255) tttttcCCCCCACAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:427394/89‑1 (MQ=255) ttttcCCCCCCCAACAAACC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc < 1:31405/90‑1 (MQ=255) tttcCCGCCGAAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:1116029/90‑1 (MQ=255) ccccccgcAAAAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg < 2:572527/86‑1 (MQ=255) ccgccgCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAGATTAAAGCCC‑CCACGTTTTGGGGGAATAGCTGCTgg > 2:288906/1‑90 (MQ=255) cccgcAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 2:83741/89‑1 (MQ=255) cccgaAAAAAA‑C‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa < 2:1555475/89‑1 (MQ=255) | TTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAA‑A‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTA > NZ_CP009273/353516‑353683 |
| 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: ‑ |