| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,509,785 | T→A | 6.7% | intergenic (‑97/‑273) | narT ← / → USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,509,785 | 0 | T | A | 6.7% | 818.0 / 35.1 | 240 | intergenic (‑97/‑273) | narT/USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (107/117); new base A (12/4); total (119/121) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.05e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01 | |||||||||||
Only 100 of 255 total aligned reads displayed.
CACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTA > USA300TCH1516_ALE/2509695‑2509875 | cACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTtat < 2:768297/91‑1 (MQ=255) ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTatat < 1:3543981/91‑1 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg < 1:438848/91‑1 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg > 2:524261/1‑91 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg > 2:524639/1‑91 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg < 2:1119079/91‑1 (MQ=255) ttCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGa < 1:1033380/91‑1 (MQ=255) tcatcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGaa < 2:2175756/91‑1 (MQ=255) catcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaaa < 1:263265/91‑1 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAt > 2:2688163/1‑91 (MQ=255) aaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAtt > 2:2813191/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc > 2:2304556/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc < 2:2061108/91‑1 (MQ=255) aTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCa > 1:2032494/1‑91 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAttttta < 2:2640356/91‑5 (MQ=37) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 2:3213755/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 2:1767212/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 2:394027/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat > 2:797617/1‑91 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:1299161/91‑1 (MQ=255) tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAatat > 1:561513/1‑91 (MQ=255) ttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAAtata > 1:2353966/1‑91 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg < 1:1512207/91‑1 (MQ=255) atttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGa < 1:2190880/91‑1 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGAc > 1:3008060/1‑91 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGAc < 1:1908371/91‑1 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 2:615156/91‑1 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 2:1900808/91‑1 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 2:2210344/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 2:1498660/91‑1 (MQ=255) ttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg < 1:2232497/91‑1 (MQ=255) ttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg > 2:2588772/1‑91 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACGTTCAATATAGACAAAGt > 1:3328899/1‑91 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTa > 2:3478205/1‑91 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 1:1983530/91‑1 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:2257654/91‑1 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:3573464/91‑1 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:704924/91‑1 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:857054/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg < 2:1442526/91‑1 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg < 2:3613596/91‑1 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:1284991/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:2455496/1‑91 (MQ=255) cAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACa < 2:2869927/91‑1 (MQ=255) tGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtt > 2:1345038/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 2:2800684/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1153114/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1423407/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:3278936/91‑1 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg > 2:3145670/1‑91 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg > 1:1572396/1‑91 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATCCAATATAGACAAAGTATTGACTACATATATATTTTATTATg < 1:1717304/91‑1 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 2:344455/1‑91 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 1:1699461/1‑91 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 2:2116319/1‑91 (MQ=255) agagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 1:1844867/1‑91 (MQ=255) gagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtgt < 1:482939/91‑1 (MQ=255) gagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtgt < 2:1572102/91‑1 (MQ=255) ggTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 1:3579190/54‑1 (MQ=255) ggTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGa < 2:1853679/91‑1 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa > 2:2540405/1‑91 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa < 2:3545913/91‑1 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:3192474/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:697184/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:1391462/1‑91 (MQ=255) tGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGt < 1:1610561/91‑1 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 1:1642480/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:298478/68‑1 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 2:3723331/1‑78 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 2:3625779/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 2:1138357/1‑91 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 1:1341622/1‑91 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 1:3640599/91‑1 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 2:492091/91‑1 (MQ=255) attgaaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa > 1:1855552/5‑91 (MQ=37) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 2:2970495/91‑1 (MQ=255) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 1:2936347/91‑1 (MQ=255) aaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg < 2:3171845/91‑1 (MQ=255) aaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg > 1:2538327/1‑91 (MQ=255) aaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAgg < 1:2693647/91‑1 (MQ=255) aaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 1:3753767/1‑91 (MQ=38) aaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 1:1192540/1‑91 (MQ=38) aaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 2:1595327/1‑91 (MQ=255) aTGTTTTTATTTATATTAAAATATTTAATATTGACAAATTTTTGTTTATATATATATTTTATTATGATTGTGTAAAAGTTAACATAATGAt < 2:2522888/91‑1 (MQ=255) tgttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtt > 2:2343442/4‑91 (MQ=38) gttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 1:3698687/3‑91 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt < 2:3528103/91‑1 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 2:2655803/1‑91 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt < 1:2896850/91‑1 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACTAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt < 1:3308626/91‑1 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat > 1:2569840/1‑59 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc < 1:2800684/91‑1 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc < 1:1396785/91‑1 (MQ=255) tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTccc < 1:797617/91‑1 (MQ=255) aTTTATATGAAAACATTCAATATAGTCAAAATATTGACAACATATATATTTTAATATGATTTTGAAAAAGTAAACATAAGGATTTTCCCtt < 2:3552099/91‑1 (MQ=255) ttATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat > 1:906368/1‑91 (MQ=255) tataTGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttatt < 1:524639/91‑1 (MQ=255) atatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattt < 2:3493984/91‑1 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTGTTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattta < 2:2999158/91‑1 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattta < 2:3692916/91‑1 (MQ=255) | CACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTA > USA300TCH1516_ALE/2509695‑2509875 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |