| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,509,782 | T→A | 5.1% | intergenic (‑94/‑276) | 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 | 2,509,782 | 0 | T | A | 5.1% | 1060.4 / 33.6 | 310 | intergenic (‑94/‑276) | narT/USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (177/117); new base A (14/2); total (191/119) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.37e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01 | |||||||||||
Only 100 of 315 total aligned reads displayed.
TTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTAT > USA300TCH1516_ALE/2509692‑2509872 | tCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTta > 1:1050210/1‑91 (MQ=255) tCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTta < 1:1271173/91‑1 (MQ=255) aCCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTtata > 2:2248491/1‑91 (MQ=255) ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTatat < 2:1142277/91‑1 (MQ=255) ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTatat < 2:2247524/91‑1 (MQ=255) catcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaaa < 1:1764013/91‑1 (MQ=255) catcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaaa < 2:2872767/91‑1 (MQ=255) atcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGaaag < 1:190811/91‑2 (MQ=255) atcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaaaa > 1:664797/1‑91 (MQ=255) atcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaaaa > 1:2127313/1‑91 (MQ=255) tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc < 2:1061836/91‑1 (MQ=255) tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc < 1:2018713/91‑1 (MQ=255) caAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACa > 2:2456203/1‑91 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAt > 2:3524558/1‑91 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAt < 2:808907/91‑1 (MQ=255) aaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAtt < 1:3826965/91‑1 (MQ=255) aTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCa > 1:1840463/1‑91 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:111377/91‑1 (MQ=255) atttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAata > 1:3247749/1‑91 (MQ=255) ttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAAtata > 2:2817997/1‑91 (MQ=255) ttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAAtata > 1:571867/1‑91 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg > 2:753743/1‑91 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg < 2:2926863/91‑1 (MQ=255) atttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGa < 2:459485/91‑1 (MQ=255) atttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGa > 1:3189430/1‑91 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGAc > 1:851162/1‑91 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 2:158428/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 1:3074491/91‑1 (MQ=255) ttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg > 1:271834/1‑91 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGt < 1:1008043/91‑1 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTa > 2:902991/1‑91 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTa > 1:1380611/1‑91 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:1651944/91‑1 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:1317775/1‑91 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:2679033/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:1952166/1‑91 (MQ=255) gATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGa > 1:1701797/1‑91 (MQ=255) atatCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTCTATGAACACATTCAATATAGACAAAGTATTGAc > 2:3261220/1‑91 (MQ=255) atatCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGat > 2:2309949/1‑90 (MQ=255) atatCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGAc > 2:1731301/1‑91 (MQ=255) cAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACa > 2:1088712/1‑91 (MQ=255) cAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACa > 1:689876/1‑91 (MQ=255) cAATACTCTGCCTATATATTAGAGCTCAATGTTATTTAAAAATGCTTTCACTTATATGAAAACATTCAATATAGACAAAGTATTGACTACa < 2:3665373/91‑1 (MQ=255) tACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatat > 1:3894981/1‑91 (MQ=255) tACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatat < 1:285471/91‑1 (MQ=255) aCTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatata > 1:1444581/1‑91 (MQ=255) ctctGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATCTGAAAACATTCAATATAGACAAAGTATTGACTACatatat > 1:1621897/1‑91 (MQ=255) cactGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatat > 1:963181/3‑91 (MQ=255) ctGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatatat < 1:1487274/91‑1 (MQ=255) tGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTATATATATAtt > 2:1755497/1‑91 (MQ=255) gCCTATATATTAGAGGTCAATGTTATTTAAAACTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAttt > 2:3887818/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTTTATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 2:1517862/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 2:2264472/1‑91 (MQ=255) cTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTtta > 2:2503353/1‑91 (MQ=255) tatataTTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat < 2:87118/91‑1 (MQ=255) atatatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttatt > 2:1162488/1‑91 (MQ=255) tatatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttatta > 1:2850470/1‑91 (MQ=255) atatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTtattat > 1:3202249/1‑91 (MQ=255) atatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTtattat > 2:3590189/1‑91 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTGTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg < 2:593949/91‑1 (MQ=255) atTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGa > 1:754837/1‑91 (MQ=255) atTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGa > 1:92692/1‑91 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 1:2449655/1‑91 (MQ=255) agagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 1:1098373/1‑91 (MQ=255) agGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtgtg > 2:2066199/1‑91 (MQ=255) agGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACAACATATATATTTTATTATGATtgtg < 2:2217763/91‑1 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa > 1:1181823/1‑91 (MQ=255) cAATGTTATTTAAAAATGCTTTCCTTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaa > 2:1189025/1‑91 (MQ=255) cAATGTTATTTAAAAATGCTTTCATTTATATGATAACCTTCAATATGGACAAAGTATTGCCGACATATATATTTTATTATGATTGTGaaaa > 1:3162751/1‑91 (MQ=255) cAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaa > 2:1815504/1‑91 (MQ=255) cAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaa > 2:2992403/1‑91 (MQ=255) cAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaa > 1:3694680/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 2:2966421/1‑91 (MQ=255) tGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGt < 2:3602874/91‑1 (MQ=255) tGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGt > 2:2792443/1‑91 (MQ=255) ttATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa > 2:1103532/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 1:2261051/1‑91 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt < 1:2156683/91‑1 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 2:2113542/1‑91 (MQ=255) attgaaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAACAAGTGAACATa > 1:3579531/5‑91 (MQ=25) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 2:2763466/91‑1 (MQ=255) aaaaaTGCTTTCAGTTATATGAAAACATTCAATATAGACAAAGGATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 1:3962411/91‑1 (MQ=255) aaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg < 1:3770717/91‑1 (MQ=255) aaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGGATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg < 1:1664567/91‑1 (MQ=255) aaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 2:3064000/1‑91 (MQ=255) tgttttCATATAAATGAAAGCATTCAATATAGACACAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtt > 2:3719033/4‑91 (MQ=38) gttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 1:3470334/3‑91 (MQ=255) gttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 2:319670/3‑91 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 2:3430393/1‑91 (MQ=255) ttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt > 1:2774140/2‑91 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt > 2:2018315/1‑91 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAATGTAAAAAAGTGAACATAAGGAtttt < 2:1242967/91‑1 (MQ=255) tttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTc > 1:3540051/1‑91 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:453134/1‑91 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:3736203/1‑91 (MQ=255) tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTccc < 2:1414252/91‑1 (MQ=255) tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTccc < 2:544807/91‑1 (MQ=255) cATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCt > 1:1295119/1‑91 (MQ=255) aTTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCtt < 2:1457488/91‑1 (MQ=255) ttATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat < 1:2562424/91‑1 (MQ=255) | TTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTAT > USA300TCH1516_ALE/2509692‑2509872 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |