| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,941,183 | 0 | T | G | 46.2% | 75.3 / 10.5 | 52 | T49P (ACC→CCC) | hdfR | HTH‑type transcriptional regulator HdfR |
| Reads supporting (aligned to +/- strand): ref base T (4/24); new base G (24/0); total (28/24) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.96e-11 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCA > NZ_CP009273/3941097‑3941262 | ggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaa > 1:300974/1‑90 (MQ=255) gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 2:556491/90‑1 (MQ=255) gcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 1:277249/90‑1 (MQ=255) ctggCCGGGGGCCCATGGGGGTTTTTGCATAAGG‑AGGAGGTTTTCCCCCGGAGGGGGTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAg < 1:958566/87‑1 (MQ=255) cTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAg < 2:2277744/90‑1 (MQ=255) cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTc < 2:235602/90‑1 (MQ=255) tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAGGGTTacac > 1:1686395/1‑90 (MQ=255) tCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACAcccc > 1:864087/1‑89 (MQ=255) cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaaa < 2:113895/77‑1 (MQ=255) cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑g < 2:853444/90‑1 (MQ=255) cATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGaaaa > 1:113895/1‑77 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCC‑GTTGAttt > 2:167304/1‑90 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa > 1:1727210/1‑69 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGaaa < 2:1727210/69‑1 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGAttt < 2:300974/90‑1 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCC‑GGTGGttt > 1:2056486/1‑90 (MQ=255) gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCC‑GGTGAttt > 2:535541/1‑90 (MQ=255) tttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCAAACCCACGTTGtttt > 1:1996072/1‑90 (MQ=255) gCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCAAACCCA‑GGTGATTTTTCAGt > 1:637458/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCC‑GTTGATTTTTCCGTTGttt > 1:1185432/1‑88 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGGAAAGGGTCACACCCA‑GCTTGTTTTTCAGtttgct > 1:1548353/1‑86 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCC‑GTTGATTTTTCAGTTTTCt > 1:744692/1‑90 (MQ=255) aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCC‑GTTGATTTTTCAGTTTTCt > 1:709835/1‑90 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTT‑ACACCCC‑GGTGGTTTTTCAGTTTTCTGGttt > 1:1461200/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGGT‑ACACCCC‑GGTGATTTTTCATTTTTCTTATTc > 2:1319060/1‑90 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTTACACCCC‑GTTGATTTTTCAGTTGTTTGAttt > 1:431950/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCC‑GTTGATTTTTCCGTTGTTTGAttt > 1:918114/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCC‑GTTGATTTTTCAGTTGTCTGAttt > 1:822584/1‑89 (MQ=255) gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGGTCACACCCA‑GTTGATTTTTCAGTTGTCTGATTc > 1:342103/1‑90 (MQ=255) gtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGaa < 1:1007415/90‑1 (MQ=255) ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGGAAAGGGTTACACCCA‑GTTGATTTTTCAGTTTTCTGATTTGAAAGCt > 1:227407/1‑90 (MQ=255) ttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGGGGAAAGGGTCACACCCA‑GGTGATTTTTCAGTTGTTTGATTTGGAAGCt > 1:1661396/1‑90 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 2:126054/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 2:1343036/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 2:1486290/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 2:637458/90‑1 (MQ=255) tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTc < 1:1252878/90‑1 (MQ=255) ggCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCActgc < 1:619883/90‑1 (MQ=255) gCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 2:342103/90‑1 (MQ=255) agggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGAc < 1:638779/88‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 2:1185432/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 2:1578280/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 2:1661396/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 2:227407/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTg < 2:431950/90‑1 (MQ=255) ggTTAAACGGATATTGTTTCTGTGGC‑GGGGGAAAAAGTTCACACCCA‑GTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTg > 1:602951/1‑90 (MQ=255) ttAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTggg < 2:744692/90‑1 (MQ=255) atatTGTTTCTGTGGC‑GGGGGAAAAAGGTTACACCCA‑GTTGGTTTTTCAGTTTTTTTGTTTTAAAGGTCACTTCTGGCTGGGGCAGAtct > 2:638779/1‑88 (MQ=255) tatTGTTTCTGTGGC‑GGGTGAAAAAAGTCACACCCC‑GTTGATTTTCCCGTTGTCTGATTCGAAAACTCACTGCTGACTGGGTCAGATaaa > 1:1576234/1‑88 (MQ=255) tatTGTTTCTGTGGC‑GGGGGAAAAGGGTCACACCCC‑GTTGATTTTTCAGTTGTCTGATTCGAAAACTCACTGCTGACTGGGGCAGATaga > 1:254016/1‑90 (MQ=255) ttCTGTGGC‑GGGGGAAAAAGGTCTCACCCA‑GTTGGTTTTTCCGTTGTTTGATTTGAAAACTCACTGCTGACTGGGGTAGATAGAGGGAtt > 1:1815931/1‑90 (MQ=255) cTGTGGC‑GGGGGAAAAAGGTCACACCCA‑GTTGATTTTTCAGTTGTCTGATTTGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCa > 1:1732030/1‑90 (MQ=255) | GGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGC‑GGGTGAAAAGGTTCACACCCA‑GTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCA > NZ_CP009273/3941097‑3941262 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |