| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,941,183 | 0 | T | G | 54.8% | 33.1 / 45.4 | 32 | T49P (ACC→CCC) | hdfR | HTH‑type transcriptional regulator HdfR |
| Reads supporting (aligned to +/- strand): ref base T (0/14); new base G (17/0); total (18/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.77e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.15e-07 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGAC > NZ_CP009273/3941106‑3941272 | ggTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTcac < 2:47504/90‑1 (MQ=255) cATGAGCGTTTCAGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACAccccc > 1:826114/1‑88 (MQ=255) gCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCAGTTGAt > 1:942233/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGTTCACACCCAGGTGATTTTTCCGtttttt > 1:835775/1‑86 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCAGTTGATTTTTCCGTTGTCt > 1:123084/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCGTTGATTTTTCCGTTGttt > 1:972327/1‑88 (MQ=255) ggCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTg < 2:1138030/90‑1 (MQ=255) cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCAGTTGATTTTTCAGTTGTCTGAt > 1:218926/1‑90 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCGTTGGTTTTTTAGTTGTTTGAttt > 2:10854/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACAACCCATTGATTTTTCCGTTGTCTTAttt > 1:1124798/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCGTTGATTTTTCAGTTGTCTGAttt > 1:79568/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTGTTTGTTTc > 2:393888/1‑90 (MQ=255) gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGaa < 1:1115046/90‑1 (MQ=255) ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTTTTTGATTTGAAAACt > 1:790948/1‑90 (MQ=255) tCACCGGCCGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 2:625386/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 1:95847/90‑1 (MQ=255) cGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGGTCACACCCCGGTGTTTTTTCCGTTTTTTGATTTGAAAAATCActg > 2:95847/1‑90 (MQ=255) cGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTTTCTGATTTGAAAGATCActg > 1:706961/1‑90 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:1203397/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:732247/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:942233/90‑1 (MQ=255) ggATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGAt < 2:917910/90‑1 (MQ=255) gATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTCCGTTGTTTGATTTGAAAACTCACTGCTGACTGGGGCAGATa > 2:384402/1‑90 (MQ=255) atatTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGATTTTTTTGTTTTTTTGTTTGAAAACTCACTGCTGACTGGGTGAGATag > 2:1107526/1‑90 (MQ=255) tatTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCCTTGGTTTTTCCGTTTTTTTATTTTAAAACTCACTGCTGCCTGGGGCAGATaga > 2:1327499/1‑90 (MQ=255) tatTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATaga < 1:782561/90‑1 (MQ=255) tatTGTTTCTGTGGC‑GGGGGGAAAAGTTTACACCCAGTTGATTTTTCAGTTGTTTGATTCGAAAGCTCACTGCTGGCTGGGGCAGATaga > 1:626461/1‑90 (MQ=255) ttGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGc < 2:972327/90‑1 (MQ=255) ttGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGc < 2:802586/90‑1 (MQ=255) gC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGc < 2:790948/90‑1 (MQ=255) gC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGc < 1:954764/90‑1 (MQ=255) c‑GGGAGGAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCTGATTTGAAAGGTCACAGCCGAATGGGTCAGATAGAGCGATTCAGCCGcg > 2:1333071/1‑89 (MQ=255) tGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGAc < 1:1263526/90‑1 (MQ=255) | GGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGAC > NZ_CP009273/3941106‑3941272 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |