| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 42.0% | 40.3 / 23.2 | 50 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| Reads supporting (aligned to +/- strand): ref base C (17/12); new base A (0/21); total (17/33) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.57e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG > NZ_CP009273/353464‑353727 | cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac > 1:239843/1‑138 (MQ=255)cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac > 1:732452/1‑138 (MQ=255)cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac > 2:451805/1‑138 (MQ=255) tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc > 1:226833/1‑139 (MQ=255) cgggCAATCCCGGCCGCAGCCCTGTGTCAGCGCCTCCCGTGATTCATTTCCCCCAACACCCGCGCATTTACCCACCCCCTTGTCCAAAAA‑TGCCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAAcc < 2:338724/137‑1 (MQ=255) cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc > 1:606963/1‑139 (MQ=255) cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc > 1:586260/1‑139 (MQ=255) ttcccggCCGCAGCCCTGTGTCAGCGGCTCCCGTGTTTCATTCCCGCAAACACCCGCCCTTTTACCCAACCCCATGTGCAAAAA‑TGCCTCCGCGGCGGCTGTCGGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGtt < 1:660913/133‑1 (MQ=18) tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct > 1:293012/1‑139 (MQ=255) tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct > 1:364501/1‑139 (MQ=255) gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc > 1:74918/1‑138 (MQ=255) gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc > 1:812740/1‑138 (MQ=255) gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt > 2:90603/1‑139 (MQ=255) ccggtgcCAGCGTCTCCCGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCAACCCCATGTGAAAAAA‑TGCCTCCGGGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTgg < 1:917033/136‑1 (MQ=255) tCAGCGCCTCCCGTGATTAATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTAAAAAAA‑TGCCTTCGGGGCGGCTGTCTGCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc < 1:497272/139‑1 (MQ=21) cggcgcCTCCCTTGATTCTTTCCCCCAAACACCCGCTCTTTTACCCACCGCCTTGTGAAAAAA‑GCCCTTCGGGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 1:554527/137‑1 (MQ=255) cAGCGGCTCCCGTAATTCATTCCCCCCAACACCCGCGCATTTACCAACCGCCTGGCAAAAAAA‑TGCCTCCGGGGCGGCTGTCGCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa < 2:606963/139‑1 (MQ=255) gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcg > 1:774909/1‑136 (MQ=255) gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAag > 1:565404/1‑139 (MQ=255) tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAaggg > 1:139546/1‑134 (MQ=255) tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑aa > 1:94814/1‑138 (MQ=255) ccccGTGATTCTTTCCCCCCAACACCCGCGCTTTTATCAACCCCCATGGAAAAAAA‑CGCCTCCGGGGCGCCTGTCTGCAGGTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa < 2:732452/137‑1 (MQ=255) ccGTGTTCCATTCCCCCCAACACCCGCGCTTTTACCAAACCCAATGTGAAAAAA‑TGCCTCCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAt < 2:475195/138‑1 (MQ=255) aTTCCCGCCAAAACCCGCCATTTTATCCAACGCCATGTAAAAAAA‑TGCCTCCGCGGGGGCTGTCTGCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGc < 1:382589/139‑1 (MQ=255) tccccccAACACCCGCCCATTTACCCACCCCCATGTGAAAAAT‑TCCCTCCGCGGGGGCTTTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGc < 1:451805/132‑1 (MQ=255) caccAAAACCCGCGCTTTTATCCAACGCCAGGTGAAAAAA‑TGCCGGCGGGGCGCCTGTCGGCCTGTTATTTTCCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc < 2:35215/137‑1 (MQ=255) cGCCAACACCCGCGCATTTATCCACCCCCATGTGCAAAAA‑TGCCTCCGCGGCGGCTGTCTCCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGAGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc < 1:824931/139‑1 (MQ=255) cGCCAACAACCGCGCTTTTACCCAACGCCATGCAAAAAAA‑TGCCTCCGGGCCGGCGGTCTGCAGTCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc < 2:289586/139‑1 (MQ=255) caacacCCGCGCTTTTACCCAACGCAATG‑GCAAAAATTGCTGTCGGGGCGCTTGTCTGCCAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg < 2:586260/139‑1 (MQ=255) caacacCCGCGCATTTACCCACCTCCATGTAAAAAAA‑TGCTATCGCGGCGTCTGTCTCCCTCCTTTTTTACCGCCGCAACAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg < 1:604302/139‑1 (MQ=255) cattACCCACCGCCGTGTTAAAAAA‑TCCCTTCGCGCCGGCTGTCTGCCACCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt < 1:96106/137‑1 (MQ=255) ttcccACCGCCATGTGCAAAAT‑TCCCTCCGCGGCGGCTGTCCGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 1:94533/135‑1 (MQ=255) tacccAACGCCATGTAAAAAAA‑CCCCTGCGCGGCGTCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg < 2:226833/135‑1 (MQ=255) aTCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGAG‑GAAAAACTTTTAACCCCCCCTTTTTTGTGGGGATCgct > 1:720512/1‑139 (MQ=25) cccAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGATTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 1:833828/138‑1 (MQ=255) cccAACCCCATGCACAAAAT‑CCCCTTCGCGGGCGCGATCGGCCAGCTTTTTTCCCGCCACAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg < 2:293012/138‑1 (MQ=255) ccATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAAAAATTTTAGCCCGCCATGTTTTGTGGGGATCgccgctcggt > 1:541730/1‑134 (MQ=37) aaaaaa‑TGCCTTCGCGGCGGCTGTCTGCCATCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt < 1:521710/137‑1 (MQ=255) ccTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAAACCC‑ACATGTTGTGGTGGAGACGCTGCTGGGAAAAAAGAGGGAAgggg > 2:514868/1‑138 (MQ=255) ccTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGACGGG‑AAAAAAATTTTAGACCCCCATGTTGTGGGGGGATCGGTGCTGGGGAAAAAGTGGGAAggg > 2:71135/1‑138 (MQ=255) cgcgGCGGCTTTCGGCCGGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg < 2:627512/137‑1 (MQ=255) cggcggCTGTCGGCCAGCTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg < 1:720429/139‑1 (MQ=255) tttGCCTGCTATTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc < 1:622715/135‑1 (MQ=255) tcggCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc < 2:191368/134‑1 (MQ=255) tCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc < 1:79097/137‑1 (MQ=255) cccgCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc < 2:929053/134‑1 (MQ=255) ttATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg < 1:337536/43‑1 (MQ=255) cTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg > 2:337536/1‑44 (MQ=255) tttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 1:661759/137‑1 (MQ=255) aTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 1:125453/138‑1 (MQ=255) aTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 2:27789/138‑1 (MQ=255) aTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc < 2:619942/138‑1 (MQ=255) tcccgcccCACCAAACCCGCCGTTCTCTCCAGTAGTGTCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg < 1:643276/136‑1 (MQ=255) | CGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG > 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 < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |