| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 51.0% | 32.1 / 74.8 | 49 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (21/3); new base A (0/25); total (21/28) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.18e-11 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.19e-09 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG > NZ_CP009273/353464‑353727 | cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac > 1:217076/1‑138 (MQ=255)cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac > 1:36870/1‑138 (MQ=255) cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa > 2:615138/1‑138 (MQ=255) tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc > 1:261288/1‑139 (MQ=255) cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc > 1:555311/1‑139 (MQ=255) cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc > 2:158796/1‑139 (MQ=255) cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc > 2:386362/1‑139 (MQ=255) tttCCACCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTC‑CCGCAAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATG‑CCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGtt < 1:329437/138‑1 (MQ=18) ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc > 1:18510/1‑139 (MQ=255) ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc > 1:246493/1‑139 (MQ=255) tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct > 2:534453/1‑139 (MQ=255) acccGCAGACCTTTGCCGGCGGCT‑CCCTTATTTATTTCCCCCCAACACCCGCCCTTTTACCCACCGCCATGTCCAAAAATG‑CTTCCGCGGCGCCTGTCGGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTtctctc < 2:601420/137‑1 (MQ=255) gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc > 1:384464/1‑138 (MQ=255) ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc > 1:184843/1‑137 (MQ=255) ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc > 2:528300/1‑137 (MQ=255) ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtatctc > 1:150095/1‑137 (MQ=255) aGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag > 1:322721/1‑139 (MQ=255) tgtCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg > 2:164777/1‑139 (MQ=255) tgtCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggc > 1:89625/1‑138 (MQ=255) gCGACTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggag > 2:425762/1‑135 (MQ=255) ggCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagg > 1:445883/1‑137 (MQ=255) cccGTTATTTATTC‑CCCCCAACACCCGCGCTTTTACCCAACCCCATG‑GGAAAAATGCCCTCCGCGGCGGCTGTCTGCCGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAt < 2:495632/138‑1 (MQ=255) cATTC‑CCCCAAACACCCGCGTATTTACCAAACGCCATGTGAAAAAATG‑CTTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTaa < 2:88006/138‑1 (MQ=255) aTTC‑CCCCCAACACCCCCGCTTTTACCCACCGCCATGGGCAAAAATG‑CCTCCGGGGCGCCTGTCTCCCAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGc < 2:582330/139‑1 (MQ=255) tttcccGCCACCAGCCGCGCATTTACCCAACGCCTTGTGAAAAAATC‑CCTGGGGGGCGCTTTTCGGCGACTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGc < 2:447970/135‑1 (MQ=255) tccccccAACACCCGCCCTTTTATCCACCCCAATGTGAAAAATGG‑CTTTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGc < 1:364599/132‑1 (MQ=255) cGCCAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCGGCAAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTc < 1:610877/139‑1 (MQ=255) cGCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTc < 1:425762/139‑1 (MQ=38) gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGGAAAAAGATTTAAAccctcc > 1:481858/1‑136 (MQ=25) caacacCCGCGTATTTCCCCACCGCCATGGACAAAAATG‑CCTCGGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtg < 2:160126/139‑1 (MQ=255) ttACCCACCCCCATGCGAAAAAACG‑CCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt < 2:18510/137‑1 (MQ=255) ttACCCAACGCCGTGTGCAAAAATG‑CTTCCGCGGGGGCTGTCTGCCAGTTATTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt < 1:196541/137‑1 (MQ=255) tacccAACGCCTTGTGAAAAAATG‑CTTTCGCGGCGGCTGTCTGCAAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 1:539151/135‑1 (MQ=255) tacccAACCCCATGTGAAAAAATG‑CCTCCGCGGGGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 1:100603/135‑1 (MQ=255) taccaaaCGCAAGGTGAAAAAACG‑CCTTGGCGGCGGTTGTCGGCCGTCTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 2:479357/133‑1 (MQ=255) tATCCACCGCCATGTGAAAAAATG‑CCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 1:246760/138‑1 (MQ=255) cccAACGCAATGCGAAAAAATC‑CTTCCGCGGCGGCTGTCTGCAATTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct < 2:538297/137‑1 (MQ=255) cccAACCCCATGCACAAAAATG‑CCTCCGGGGCGGCTGTCTGCCGGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct < 2:143874/137‑1 (MQ=255) cGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGGAAAAAAATTTAA‑CACCCCCTGTTTTGTGGGGATCGCTGCTggg > 2:548535/1‑138 (MQ=21) cGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑GAAATAGATTTTAACCCCCCATTTTTTGTGGGGATCGCTGCTggg > 1:521780/1‑138 (MQ=37) tgtgCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAAATTTTAACCCCTCCTGTTTTGTGGGCAGCGCTGCTGGTaaaa > 1:75848/1‑136 (MQ=25) agaaaaaaTG‑CCTTGGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg < 2:548033/136‑1 (MQ=255) aaaaaaTG‑CCTTCGCGGCGGCTGTCTGCCACTTATTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt < 1:505239/137‑1 (MQ=255) aaaTG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAACATTAAAACCCCCCTCTTTTTTGGGGATCGCTGGTGGTGAAAACGTggg > 2:359818/1‑137 (MQ=255) ccTCCGGGGCGGCTGTCTGCCAGCTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg < 2:184843/138‑1 (MQ=255) ccTCCGCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg < 1:191770/138‑1 (MQ=255) ctCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc < 1:197026/137‑1 (MQ=255) tttctcccgccaAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 2:56014/132‑1 (MQ=255) ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 1:386362/137‑1 (MQ=255) tttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg < 1:543200/138‑1 (MQ=255) tttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg < 2:521780/138‑1 (MQ=255) tcccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg < 2:75848/136‑1 (MQ=255) | CGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG > NZ_CP009273/353464‑353727 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |