| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,350,458 | 0 | T | G | 52.8% | 45.9 / 70.5 | 53 | T304P (ACC→CCC) | sapA | peptide ABC transporter substrate‑binding protein SapA |
| Reads supporting (aligned to +/- strand): ref base T (2/23); new base G (28/0); total (30/23) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.81e-13 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.07e-09 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTG > NZ_CP009273/1350369‑1350543 | ataataGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGgt < 1:2892615/90‑1 (MQ=255) taGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTa < 1:396794/90‑1 (MQ=255) tGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GGTTTT‑GGGGGGGTTaatg > 2:401251/1‑88 (MQ=255) tGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGGGGGGGTAAATg > 1:1934664/1‑90 (MQ=255) tGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGCGGGGTTaaaag > 1:549323/1‑88 (MQ=255) tGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGCGGGGGTaaaat > 1:2880581/1‑88 (MQ=255) ggATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGGGGGGGTTAATgg > 1:3112393/1‑89 (MQ=255) gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGG‑TTT‑GGGGGGGTTAAAtac > 2:939569/1‑88 (MQ=255) gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGcc > 1:549367/1‑90 (MQ=255) gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGcc < 1:3267557/90‑1 (MQ=255) gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGGTAAATTcc > 1:2925931/1‑90 (MQ=255) gATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGGTAAATAcc > 2:1142325/1‑90 (MQ=255) aTTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGG‑TTT‑GGGGGGGGTAAATggc > 2:554115/1‑88 (MQ=255) aTTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GGTTTT‑GGGGGGGTTAAATGcc > 1:2478303/1‑90 (MQ=255) aTCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGCGGGGTTTAATGCCAGATAg > 1:2488963/1‑90 (MQ=255) ggCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTTGGGGGGGGTTAAAT‑ACACATAGGCgg > 1:2862068/1‑89 (MQ=255) ggCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGa < 2:2145536/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 1:1786295/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 2:549367/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 2:2855105/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 2:2577136/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 1:1519772/90‑1 (MQ=255) tGGTTATTAATCGCCAGTGCCAGAGCATGGCGGACAGCGGGATTATTTATCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTc < 2:637520/90‑1 (MQ=255) ggTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGGTAAAAGGCACATAGgcggcggtta > 1:2513141/1‑86 (MQ=255) gTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCAt < 1:1142325/90‑1 (MQ=255) attaATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGCGGG‑TTT‑GGGGGGGTT‑AATGCCAGATAGGGGGCGGTTATccc > 2:1519772/1‑90 (MQ=255) ttaATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGGGGGGTTTAATGCCAGATAGGGGACGTTTATcccc > 1:1604658/1‑89 (MQ=255) cGCCAGTGCCATCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGTTTAATGGCCGGTAGGGGAGGGTCAGTCCacgacg > 1:3116084/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGGGGGGTTTAATGCCAGATAGGCGGCGGTCATCCCCGGACg > 1:3372475/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGGGGGGGTATATACCCGATAAGGGACGTTCATCCCAGGACg > 2:1474891/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGCGGGGGTTAATTCCAGATAAGGGGCGTTTATCCCCCGACg > 2:2877697/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGGGGGGGTTAATGGCAGAAAGGGGGCGGTCATCCCCCGACg > 2:2993154/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGGGGGGGTAAATGCCAGATAGGCGACGGTCATCCCCGGACg > 1:1605299/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGTTAAATGCCAGAAAGGCGACGTTCATCCCCGGACg > 1:2481140/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGGTAAATGCCAGATAGGCGGCGGTCATCCCCGGACg > 1:331334/1‑90 (MQ=255) cGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGGGGTAAATGCCAGAAAAGGGGCGTTCATCCCCGGACg > 1:3372037/1‑90 (MQ=255) gCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGGGGGGGTTAATGCCAGGTAGGGGGCGGTCATCCCAGGAGGc > 1:516489/1‑90 (MQ=255) aGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑TGGGGGGGTAAAAACCCGAAAGGGGGCGGTCATCCCCGGGcgccgc > 2:1755638/1‑90 (MQ=255) cGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGgtcgt < 2:3088543/90‑1 (MQ=255) gggATTATTTAGCGGC‑GG‑TTT‑TGCGGGGTTTAAAACCCGGAAGGCGGGGTTTATCCCCCGGCGCCGGGTGTAACGCAAAGGCGGggcggc > 2:194962/1‑88 (MQ=255) gATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCAc < 2:331334/90‑1 (MQ=255) attattTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACg < 1:2993154/90‑1 (MQ=255) attattTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACg < 1:2944297/90‑1 (MQ=255) attattTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACg < 1:1474891/90‑1 (MQ=255) ttattTAGCGGC‑GG‑TTT‑TGCGGGGTTTAATTCCAAAAAGGCGACGGTCATCCCCGGACGCAGCGGTAAAAACAAACGCGGGGGGTCCCGc > 1:1650143/1‑90 (MQ=255) attTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCaa < 2:1934664/90‑1 (MQ=255) attTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCaa < 2:2142310/90‑1 (MQ=255) attTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCaa < 2:3227354/90‑1 (MQ=255) aGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATg < 2:2235976/90‑1 (MQ=255) aGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATg < 2:1140556/90‑1 (MQ=255) gcggc‑gG‑TTT‑TGGGGGGTTTAAAGCCCGAAAGGGGGCGGTCATCCCAGGACGCAGCGGTAAACGCAAGCGGGGGGCGGCAAGCCAAAAgg > 1:556127/1‑90 (MQ=255) gg‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAgc < 2:1605299/90‑1 (MQ=255) gg‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAgc < 2:2318760/90‑1 (MQ=255) gCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGAGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAgctggctg < 1:1073091/90‑1 (MQ=255) | ATAATAGATGGATTGCATCAGGCGCTGGTTATTAATCGCCAGTGCCAGCGCATGGCGGACAGCGGGATTATTTAGCGGC‑GG‑TTT‑GGCGGTGTTAAATGCCAGATAGGCGACGTTCATCCCAGGACGCAGCGTTAAACGCAAGCGCGGGTCGTCACGCAAAATGGATAGCTGGCTG > NZ_CP009273/1350369‑1350543 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |