| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.4% | 100.4 / 22.5 | 56 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| Reads supporting (aligned to +/- strand): ref base A (39/0); new base C (0/17); total (39/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.02e-14 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAT > NC_000913/2001779‑2002048 | agTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGaaaaaaa > 1:1171762/1‑140 (MQ=255) aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCccg > 2:1294669/1‑140 (MQ=255) aTAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTgg > 2:51085/1‑140 (MQ=255) cctggtttATATGATTTATGGGCATGATTTTCCGTTTCTGCAGGGTTTTTAATG‑GGACGTTTGGTGGGTGAAAGGGGGGTTTTTTTGGGGG‑TTAAAGGTAATTCCCGGGAAGAAAAAACCCCCGCCGGTGGC‑GGGGAAGc < 2:762735/134‑1 (MQ=255) ccTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGc > 2:1396521/1‑140 (MQ=255) tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCAc > 2:662842/1‑140 (MQ=255) cGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGt > 1:539953/1‑140 (MQ=255) tataTGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGc > 1:499876/1‑140 (MQ=255) tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTg > 1:1178640/1‑140 (MQ=255) aggtgTTTTCGGTTTGTTTTTCTGTTCCGGCGGGTTTTTTAAGG‑GGACTTTTAGTGGGTAAAATGAGGGTTTATTTGGGGG‑TTGCGGGTAAACTCGGGTCAGAAAAAACCTCCGCCGGTGGC‑GGGGAAGCACGTTGCTGa < 2:1273489/136‑1 (MQ=255) gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACaaa > 1:1278361/1‑140 (MQ=255) gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACaaa > 1:1233695/1‑140 (MQ=255) gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACaaa > 1:1146467/1‑140 (MQ=255) gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACaaa > 1:205334/1‑140 (MQ=255) gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACaaa > 1:627144/1‑140 (MQ=255) aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTg > 2:1412133/1‑140 (MQ=255) aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTg > 2:408808/1‑140 (MQ=255) cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTgcg > 2:1379590/1‑140 (MQ=255) cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTgcg > 2:552704/1‑140 (MQ=255) gATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTAt > 2:130058/1‑140 (MQ=255) gTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCgg > 2:1308078/1‑140 (MQ=255) ttCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt > 2:785099/1‑140 (MQ=255) ttCTGC‑GGGTTTTTAAACGGGACGATTGGGGGGTAAAATGGGGGGTTTTTGGGGGG‑TTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt < 2:627144/140‑1 (MQ=255) cTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgc > 1:793816/1‑140 (MQ=255) tggggggTTTTTAAAC‑GGGAGATTAGGGGGGAAAATGGGGGGTTTTTTGGGGG‑TTACAGGAAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcg < 2:705213/136‑1 (MQ=255) gcggggTTTTTAATC‑GGACGATTAGGGGGTGAAATGGGGGTTTTTTGGGGGG‑TTACAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcgg < 2:1278361/137‑1 (MQ=255) cAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggc > 1:1470517/1‑140 (MQ=255) gggTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGt > 1:839477/1‑140 (MQ=255) gttttttAATG‑GGAGGATTAGTGGGTAAAAGGAGGGTTTATTTGGGGG‑TTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTa < 2:1178640/138‑1 (MQ=255) tttttAATC‑GGACGATTAGTGGGTGAAATGAGGGGCTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAACACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaaa > 2:919768/1‑140 (MQ=255) c‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCCGCGTAAACGCCTTAt > 1:470088/1‑140 (MQ=255) gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc > 1:584809/1‑140 (MQ=255) gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc > 2:164730/1‑140 (MQ=255) acaaTTAGGGGGTAAAATGGGGGTTTATTGGGGGG‑TTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg < 2:1171762/137‑1 (MQ=37) aCGATTAGTGGGTGAAATGAGGGGTTATTGGGGGG‑TTACAGGTAAATCCCGGGCAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg < 1:1135114/140‑1 (MQ=39) aCGATTAGTGGGAAAAATGAGGGTTTATTGGGGGG‑TTACAGGAAAATCCCAGGCAGAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg < 2:1233695/140‑1 (MQ=38) gtttAGGGGGTGAAATGGGGGTTTATTGGGGGG‑TTAAAGGTAATTTCCAGGCAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGc < 2:839477/138‑1 (MQ=38) gATTGGGGGGTGAAATGAGGGTTTATTTGGGGG‑TTAAAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGc < 2:205334/140‑1 (MQ=38) ggTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa > 1:510500/1‑140 (MQ=255) tGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAt > 1:1300736/1‑140 (MQ=255) acaTGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACACCTTATCCGGCCTACAAAAAtgt > 2:802633/3‑140 (MQ=255) aaaTGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgt > 1:1018321/1‑140 (MQ=255) gAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAA‑CCCGGCGGTGGCGGGGGAAGCACGTTCTTGACAAATTGCGCTTTATGTGCCCGGTGGCGGCGAAAACCCCTAATCCGGCCTAAAAAAAttgccaa > 2:1157990/1‑134 (MQ=255) gggTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAtt > 1:80593/1‑140 (MQ=255) ttATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCaa > 1:1460055/1‑140 (MQ=255) tttGGGGGTTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa < 2:1300736/140‑1 (MQ=37) gg‑TTACAGATAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCa < 2:172398/140‑1 (MQ=255) g‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa > 2:447474/1‑140 (MQ=255) g‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa > 1:952903/1‑140 (MQ=255) g‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa > 1:172398/1‑140 (MQ=255) ttACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAt < 1:408808/140‑1 (MQ=255) agggaaaaTCCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa < 2:847863/135‑1 (MQ=37) aaGGAAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCCGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa < 2:470088/139‑1 (MQ=37) ccgggaaGAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc < 2:657281/134‑1 (MQ=255) cAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGcc > 1:249586/1‑140 (MQ=255) ggCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGccct > 1:847863/1‑138 (MQ=255) ggCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg > 1:107020/1‑140 (MQ=255) ggCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg > 2:503158/1‑140 (MQ=255) caaaaaaaacCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt < 1:687682/137‑1 (MQ=255) cAGAAAAAACCCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt < 2:539953/140‑1 (MQ=255) | AGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATC‑GGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGC‑GGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAT > NC_000913/2001779‑2002048 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |