| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,509,782 | T→A | 6.5% | 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 | 6.5% | 835.7 / 34.9 | 246 | intergenic (‑94/‑276) | narT/USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (109/121); new base A (12/4); total (121/125) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.93e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.21e-01 | |||||||||||
Only 100 of 250 total aligned reads displayed.
TTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTAT > USA300TCH1516_ALE/2509692‑2509872 | tCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTta < 1:807184/91‑1 (MQ=255) tCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTta > 1:65966/1‑91 (MQ=255) cACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTtat < 2:768297/91‑1 (MQ=255) ccTTTATCAATATCATTTATTTTTTAATATATATCAATACTCTGCCTATATATTAGAGGTAAATGTTATTTAAAAATGCTTTCATTTatat < 2:1594188/91‑1 (MQ=255) ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTatat < 2:3328863/91‑1 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg < 2:1119079/91‑1 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg > 2:524261/1‑91 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg < 1:438848/91‑1 (MQ=255) cTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATg < 1:2012752/91‑1 (MQ=255) ttCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGa < 1:1033380/91‑1 (MQ=255) ttCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGa > 1:3346644/1‑91 (MQ=255) tcatcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaa < 2:2807724/91‑1 (MQ=255) tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc < 2:1860684/91‑1 (MQ=255) caAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACa < 2:2642215/91‑1 (MQ=255) caAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACa < 2:2993338/91‑1 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATATAAATGAAAGCAt < 1:167491/91‑1 (MQ=255) aaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAtt < 1:3680518/91‑1 (MQ=255) aaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAtt > 2:2813191/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc > 2:2053694/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc > 1:2326875/1‑91 (MQ=255) aTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCa > 1:2609251/1‑91 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:1299161/91‑1 (MQ=255) ttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAAtata < 2:2456935/91‑1 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg < 1:1609379/91‑1 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg < 1:1512207/91‑1 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg > 2:2180004/1‑91 (MQ=255) atttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGa < 2:3270420/91‑1 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 1:251861/91‑1 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 2:615156/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 1:277496/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 2:1499144/91‑1 (MQ=255) ttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg < 1:2231995/91‑1 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGt < 2:145438/91‑1 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGt < 2:2247699/91‑1 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTa < 1:284372/91‑1 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTa < 2:2162982/91‑1 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 1:1983530/91‑1 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:3573464/91‑1 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:857054/1‑91 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:2631892/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg < 1:1904570/91‑1 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:1284991/1‑91 (MQ=255) gATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGa > 2:2904036/1‑91 (MQ=255) cAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTATCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACa > 2:3478847/1‑91 (MQ=255) aaTACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACat > 2:2714533/1‑91 (MQ=255) aaTACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTGCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACat > 1:3088274/1‑91 (MQ=255) aCTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatata < 2:1132661/91‑1 (MQ=255) ctctGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatat < 2:553568/91‑1 (MQ=255) tGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtt > 2:1345038/1‑91 (MQ=255) tGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtt > 1:1832906/1‑91 (MQ=255) gCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAttt > 1:3309504/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACTAAGTATTGACTACATATATAtttt > 2:3616497/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1153114/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:2092765/91‑1 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1423407/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:160299/91‑1 (MQ=255) cTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTtta > 2:71045/1‑91 (MQ=255) tatataTTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat < 2:1395345/91‑1 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg > 1:1572396/1‑91 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATCCAATATAGACAAAGTATTGACTACATATATATTTTATTATg < 1:1717304/91‑1 (MQ=255) atTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGa < 1:2691648/91‑1 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 2:383767/1‑91 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 1:218960/1‑91 (MQ=255) agagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 1:3546718/1‑91 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa < 2:3545913/91‑1 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa > 2:2539085/1‑91 (MQ=255) gTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa < 2:2672357/91‑1 (MQ=255) cAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaa > 1:3223171/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:1391462/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:697184/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:830992/1‑91 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg < 1:3586035/91‑1 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 1:2933942/1‑91 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 1:1642480/1‑91 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 2:320087/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:298478/1‑68 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg < 1:3722837/78‑1 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 2:3723331/1‑78 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 2:3625779/1‑91 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt < 1:583947/91‑1 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 1:1341622/1‑91 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 2:227832/1‑91 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 2:492325/91‑1 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa > 2:3473726/1‑91 (MQ=255) tAAAAATGCTTTCATTTATATGAAAAAATTCAATATAGACAGAGTATTGGCTACATATATATTTTATAATAAATATGAAAAAGTGAACATa < 2:1794685/91‑1 (MQ=255) attgaaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa > 1:1855552/5‑91 (MQ=37) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 2:2970495/91‑1 (MQ=255) aaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAgg < 1:2393345/91‑1 (MQ=255) aaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAgg > 1:391108/1‑91 (MQ=255) aaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 1:1192540/1‑91 (MQ=38) tgttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtt > 2:813788/4‑91 (MQ=38) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt < 2:3528452/91‑1 (MQ=255) ttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt > 2:3166588/2‑91 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat < 2:2569839/59‑1 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat > 1:2569839/1‑59 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc < 1:1396785/91‑1 (MQ=255) ttCATATAAATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:545450/1‑91 (MQ=255) tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTccc > 2:3554157/1‑91 (MQ=255) aTTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCtt < 2:2326875/91‑1 (MQ=255) ttATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat < 2:3008060/91‑1 (MQ=255) | TTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTAT > USA300TCH1516_ALE/2509692‑2509872 |
| 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: ‑ |