| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,941,183 | 0 | T | G | 60.6% | 25.0 / 41.2 | 33 | T49P (ACC→CCC) | hdfR | HTH‑type transcriptional regulator HdfR |
| Reads supporting (aligned to +/- strand): ref base T (0/13); new base G (20/0); total (20/13) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.74e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.43e-07 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCT > NZ_CP009273/3941097‑3941268 | ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaa > 2:255070/1‑90 (MQ=255)ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaa > 1:918019/1‑90 (MQ=255)ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaa > 2:1043777/1‑90 (MQ=255) ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaaa < 1:756828/90‑1 (MQ=255) cTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAg < 1:605455/90‑1 (MQ=255) cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGGTCACAccccg > 2:293798/1‑88 (MQ=255) tGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGtt < 1:370934/90‑1 (MQ=255) tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCAGTTGGtttt > 2:964321/1‑90 (MQ=255) ttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCCTTGAttttt > 2:804266/1‑89 (MQ=255) tGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAg < 1:1043777/90‑1 (MQ=255) aTAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCCGTGATTTTTCCGTTg > 2:829274/1‑90 (MQ=255) aTAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCAGTTGATTTTTCAGTTg > 2:228023/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCATTGATTTTTCAGTTTTCt > 1:1071335/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGGTCACACCCCGTTGGTTTTTTAGtttttt > 1:1002137/1‑86 (MQ=255) cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCAGTGATTTTTCAGTTTTCTGAt > 1:783524/1‑90 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCGTTGGTTTTTCCGTTTTCTGAttt > 2:631945/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTTACACCCCGTTGGTTTTTCAGTTGTCTGAttt > 2:402963/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCCGTTGATTTTTCAGTTGTCTGtttt > 2:61348/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCCATTTTCTGAttt > 2:1082474/1‑89 (MQ=255) gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGaa < 1:1032488/90‑1 (MQ=255) gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGaa < 2:165200/90‑1 (MQ=255) ggCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCActgc > 2:188635/1‑90 (MQ=255) ggCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTTGAAAGCTCActgc > 2:323747/1‑90 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:631945/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:818351/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:918019/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 1:403117/90‑1 (MQ=255) gTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTTTGTTTTGAAAACTCACTGCTGACTgg > 2:996676/1‑90 (MQ=255) acagcGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGt < 2:797621/86‑1 (MQ=255) gATATTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCCGTTGATTTTTCCGTTTTTTGATTCGAAAGCTCACTGCTGGCTGGGGGAGATa > 2:980092/1‑90 (MQ=255) gTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGa < 1:375710/90‑1 (MQ=255) tgtgGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTGTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTTAg > 2:105885/1‑90 (MQ=255) c‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCt < 1:909143/90‑1 (MQ=255) | GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCT > NZ_CP009273/3941097‑3941268 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |