| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,941,183 | 0 | T | G | 52.3% | 52.8 / 68.3 | 44 | T49P (ACC→CCC) | hdfR | HTH‑type transcriptional regulator HdfR |
| Reads supporting (aligned to +/- strand): ref base T (2/19); new base G (23/0); total (25/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.49e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-08 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGC > NZ_CP009273/3941097‑3941267 | ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaa > 2:190689/1‑90 (MQ=255)ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaa > 2:225065/1‑90 (MQ=255) gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 1:190689/90‑1 (MQ=255) gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 1:1200251/90‑1 (MQ=255) ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaaa < 1:17572/90‑1 (MQ=255) cTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAg < 1:1807616/90‑1 (MQ=255) tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTacac > 2:1070424/1‑90 (MQ=255) tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCacac > 2:1873455/1‑90 (MQ=255) tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCa > 2:1010775/1‑90 (MQ=255) gAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTg < 1:1274213/90‑1 (MQ=255) aGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCAGTTGa > 2:786007/1‑90 (MQ=255) gCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAGGGTTCCACCCCGtttgt > 2:593823/1‑87 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑AAACCCACTTGGTTTTTCAGttttgt > 1:1623020/1‑86 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAGGTTCACACCCCGTTGATTTTTCCGTTTTCt > 2:674925/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCCTTGGTTTTTCAGTTGttt > 2:320910/1‑88 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGGAAAAGTTCACACCCCATTGATTTTTCACTTGTCTGAttt > 2:1086596/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCCGTTGGTTTTTCCGTTGTTTGGttt > 2:1506134/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCCATTGGTTTTTCAGTTGTCTGtttt > 1:1050122/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCGTTGATTTTTCAGTTGTTTGAttt > 2:1648507/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGGTGGTTTTTCACTTGTCTTAttt > 2:1176704/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCCGTTTTCTGAttt > 2:1590682/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCCATTGTCTTAttt > 2:313237/1‑89 (MQ=255) gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGaa < 1:1692330/90‑1 (MQ=255) ttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTTTTATTTGaaaa > 2:627046/1‑89 (MQ=255) ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCt < 1:627046/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 1:305565/90‑1 (MQ=255) ggCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGGTCACACCCCGGTGATTTTTCAGTTGTTTTTTTTGAAAACTCActgc > 2:1672531/1‑90 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:513046/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1027391/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1070424/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1338979/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1590682/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:1652366/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1873455/90‑1 (MQ=255) cGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACt < 1:1506134/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 1:1703834/90‑1 (MQ=255) gATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCCGTTGATTTTTCAGTTGTTTTATTCGAAAACTCAATTCTGACGGGGGCAggaa > 2:912251/1‑87 (MQ=255) gATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGGTGATTTTTCAGTTTTCTGTTTTGAAAAATCACTGCTGACTGGGGCAGATa > 2:1473813/1‑90 (MQ=255) tatTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATaga > 2:554805/1‑90 (MQ=255) gTTTCTGTGGC‑GGGGGGAAAGGGTTACACCCACGTGATTTTTCCGTTTTTTGGTTTGAAAAATCACCGCTGACTGGGGCAGATAGAGCgg > 1:1564088/1‑89 (MQ=255) gTTTCTGTGGC‑GGGGGGAAAAGGTCACACCCCCGTGATTTTTCAGTTTTTTTTTTTGAAAAATCACTGCTGACTGGGGGAGATagagagg > 1:1515069/1‑87 (MQ=255) cTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCCGTTGTTTGATTTGGAAAGTCACTGCTTAATGGGGGGGAAAGAGCGATTCa > 2:1540429/1‑90 (MQ=255) gC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGCCTGGGTCAGATAGAGCGATTCAGCCGc < 1:811060/90‑1 (MQ=255) gC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGc < 1:1884027/90‑1 (MQ=255) | GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGC > NZ_CP009273/3941097‑3941267 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |