| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,001,911 | 0 | G | A | 41.8% | 62.0 / 27.2 | 55 | intergenic (‑122/+199) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| Reads supporting (aligned to +/- strand): ref base G (26/6); new base A (0/23); total (26/29) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.88e-10 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
TTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC > NC_000913/2001766‑2002054 | ttCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGaaaa > 1:971588/1‑150 (MQ=255) cGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑ccc < 1:196770/151‑1 (MQ=255) ataGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCccgc < 1:880892/150‑1 (MQ=255) ataGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCccgc < 1:426361/150‑1 (MQ=255) agagTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATGCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCccgccg > 2:455677/1‑150 (MQ=255) tGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTgg > 2:69557/1‑150 (MQ=255) tCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCgggg > 1:251865/1‑150 (MQ=255) aCGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGa > 2:160949/1‑149 (MQ=255) aacagccggggtttATATGAGTTAGCGGCATGTTTTTCGGTTTCTGAGGGTTTTTTAAGGGGAGGTTTAGGGGGTAAAATGGGGGTTTATTGGGGGG‑TAACAGTTAATTC‑CCGGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGtt < 2:571831/139‑1 (MQ=255) aGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCt > 2:909505/1‑151 (MQ=255) cccTGCTTTATATGAGTTATCGGAATGATTACCCGTTTCTGAAGGTTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGTTTTTTGGGGGT‑TTACAGGTAAATC‑CCGGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTg < 1:568499/150‑1 (MQ=255) tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACa > 2:177888/1‑150 (MQ=255) gCGTTTTAGGATTTATGGGAATGATTACCGTTTTCTGCAGGTTTTTAAATGGGACGATTAGGGGGTGAAAGGGGGGTTTTTTGGGGGG‑TTACAGGAAATTC‑CCAGGAAAAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaa < 2:363844/150‑1 (MQ=255) gTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt > 1:421857/1‑151 (MQ=255) ttATATGATTTATCGGCATGATTATCCGTTTCTGAGGGGTTTTTAATCGGACGATTAGGGGGTAAAATG‑GGGGTTTTTTGGGGGTTTACAGGTAAATT‑CCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACa < 1:868124/146‑1 (MQ=255) ttATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg > 1:866567/1‑151 (MQ=255) tataTGAGTTATCGGCATGATTATCCGTTTCGGCGGGGTTTTTAATCGGACGATTGGGGGGTAAAAGGGGGGTTTATTGGGGGT‑TTACGGGTAAATT‑CCGGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg < 1:738656/150‑1 (MQ=255) tataGGAGTTATCGGCATGATTATCCTTTACTGCGGGTTTTTTAAGGGGACGATTAGGGGGGGAAAGGGGGGTTTTTTGGGGGG‑TTACAGGTAAATT‑CCGGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg < 1:968175/150‑1 (MQ=255) tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcgc > 1:890376/1‑151 (MQ=255) gAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt > 1:741211/1‑151 (MQ=255) ttaggggCATGTTTTTCCTTTTCTGCGGTTTTTTTAATCGGACGATTGGGGGGTGAAA‑GGGGGGTTTTTTGGGGGTTTAAAGATAAATC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt < 2:971503/143‑1 (MQ=255) ttATAGGGAGGATTATCGGTTTCGGCGGGTTTTTTAATGGGGCAATGAGGGGGAGAAATGAGGGGTTTTTGGGGGT‑TTACAGGAAAATG‑CGGGGGAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCttt < 1:476153/148‑1 (MQ=255) ggtaTGTTTATCCTTTTCTGGGGGTTTTTTAATCGGCCGATTGGGGGGTAAAAGGGGGGGTTATTGGGGGG‑TTAAAGGAAATTC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGt < 2:329238/144‑1 (MQ=255) ggCATGATTTTCCGTTTCGGAAGGTTTTTAAATGGGACGATGAGGGGGAGAAAGGAGGGTTTATTTGGGGT‑TTAGAGGTAATTT‑CCGGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATg < 1:523375/146‑1 (MQ=255) gCATGATTATCCGTTTCTGCAGGTTTTTTAATCGGACGATTAGTGGGTAAAATGGGGGGTTATTGGGGGG‑TTACAGGTAAATC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCg < 2:726413/151‑1 (MQ=255) tGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt > 1:916134/1‑151 (MQ=255) ttttCCGTTTCTGCAGGTTTTTTAACCGGACGATTAGGGGGTAAAAGGAGGGTTTTTTGGGGGT‑TTACAGGAAAATC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgc < 1:52196/147‑1 (MQ=255) ttACCCTTTTCTGCGGGTTTTTTAATGGGACGATTGGGGGGTAAAATGGGGGTTTATTGGGGGT‑TTACAGGTAAATC‑CCAGGAAAAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCgg < 1:588942/146‑1 (MQ=255) aTCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggc > 2:221830/1‑151 (MQ=255) cGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggcg > 2:734664/1‑149 (MQ=255) tttCTGCAGGGTTTTTAAGGGGCGGTTTAGTGGGTGAAATGGGGGGTTA‑TTGGGGG‑GTAAAGGTTAATTCCCAGGCAGAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGt < 2:479237/148‑1 (MQ=255) ttttAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCgg > 2:398586/1‑151 (MQ=255) tttAAACGGACGATGAGGGGGTGAAATAGGGAATTATGGGGGGG‑TCGCTGAAAAATT‑CCAGGAAGAAAAACT‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGCCAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCgg < 2:207914/150‑1 (MQ=255) aaTCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCt > 1:685334/1‑150 (MQ=255) aTCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTAc > 2:794095/1‑151 (MQ=255) ttggggggTAAAAGGAGGGGTTTTTGGGGGT‑TTACAGATAAATC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgt < 1:672351/145‑1 (MQ=37) tAGTGGGTGAAATGAGGGTTTATTTGGGGG‑TTACAGGAAAATT‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgtg < 1:342565/150‑1 (MQ=255) ggggttaaaaTGGGGGTTTGTTGGGGGG‑TTGCAGG‑AAAGT‑CCCGGAAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCaa < 2:805634/144‑1 (MQ=25) tGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc > 1:956225/1‑150 (MQ=255) aaaTGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑GCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAAt > 1:175468/1‑151 (MQ=255) aaatgggggTTTTTTGGGGGTTTACAGG‑AAATT‑CCCGGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc < 1:870211/143‑1 (MQ=25) gggggtTTATTGGGGGG‑TTAAAGGAAAATT‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATaa < 2:229693/147‑1 (MQ=37) gggtTTTTTTGGGGG‑TTACAGGTAAATC‑CCAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATaaa < 2:502278/148‑1 (MQ=255) ttATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAt > 1:373166/1‑151 (MQ=255) tttGGGGT‑TTACAGGTAAATA‑CC‑GGCAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc < 1:780584/150‑1 (MQ=37) tttGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc > 2:593567/1‑150 (MQ=255) tGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAAc > 1:595512/1‑151 (MQ=255) gggg‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACtt > 1:410910/1‑151 (MQ=255) ggg‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg > 1:448152/1‑151 (MQ=255) taaagtaaaaTT‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAg < 2:523249/143‑1 (MQ=37) aaaTC‑CCAGGAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATa < 2:645851/151‑1 (MQ=255) aaaTC‑CCAGAAAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg < 2:989003/148‑1 (MQ=255) aTT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATa > 1:156718/1‑149 (MQ=255) cAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc > 2:436156/1‑150 (MQ=255) cAGGCAAAAAAAAC‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAag < 1:320278/147‑1 (MQ=255) | TTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TTACAGGTAAATT‑CCAGGCAGAAAAAAA‑CCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC > NC_000913/2001766‑2002054 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |