| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,941,183 | 0 | T | G | 60.0% | 12.1 / 21.1 | 20 | T49P (ACC→CCC) | hdfR | HTH‑type transcriptional regulator HdfR |
| Reads supporting (aligned to +/- strand): ref base T (1/7); new base G (12/0); total (13/7) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.03e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCA > NZ_CP009273/3941099‑3941262 | ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaaa < 1:427318/90‑1 (MQ=255) tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTTCCAAccc > 2:316608/1‑90 (MQ=255) tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAAGGTCAAAcccc > 2:86415/1‑89 (MQ=255) tGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGtt < 1:177957/90‑1 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 1:341420/58‑1 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa > 2:341420/1‑58 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGTTCACACCCAGTTGATTTTTCAGTTGTCt > 2:122230/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCAGTTTTTTTTTCAGTTGTCt > 2:507869/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCCGTTGGTTTTTCCGtttttt > 2:488926/1‑86 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCAGTTGATTTTTCAGtttttt > 2:435032/1‑86 (MQ=255) cAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGAt < 2:65469/90‑1 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGTTGGTTTTTCCGTTGTCTTAttt > 2:167340/1‑89 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:488926/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:260876/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCCGTTGATTTTTCCGTTTTTTGTTTTGGAAAATCACTGCTGACTg > 1:128682/1‑90 (MQ=255) tAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGt < 1:525569/90‑1 (MQ=255) tatTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCAGTTGATTTTTCAGTTGTTTTTTTCGAAAACTCACTGCTGACTGGGTCAGATaga > 2:521046/1‑90 (MQ=255) gTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCCGGTGATTTTCCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATAGAGGGa > 2:202455/1‑90 (MQ=255) cTGTGGC‑GGGGGAAAAGGTTCACACCCCGTTGATTTTTCCGTTGTCTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTCa > 2:370979/1‑90 (MQ=255) cTGTGGC‑GGGGGAAAAAGTTCACACCCCGTTGATTTTTCCGTTGTTTTTTTTGAAAACTCACTGCTGACTGGGGCAGATAAAGCGATTCa > 1:375409/1‑90 (MQ=255) | CCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCA > NZ_CP009273/3941099‑3941262 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |