| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,509,792 | A→G | 6.3% | intergenic (‑104/‑266) | 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 | 2,509,792 | 0 | A | G | 6.3% | 744.9 / 28.2 | 240 | intergenic (‑104/‑266) | narT/USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (106/118); new base G (12/3); total (118/122) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.64e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 | |||||||||||
Only 100 of 257 total aligned reads displayed.
TCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTG > USA300TCH1516_ALE/2509703‑2509882 | tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc > 1:2024223/1‑91 (MQ=255)tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc < 2:3518058/91‑1 (MQ=255)tcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAAc < 2:1860684/91‑1 (MQ=255) caAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACa < 1:2306113/91‑1 (MQ=255) caAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACa < 2:2993338/91‑1 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAt > 2:2688163/1‑91 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATATAAATGAAAGCAt < 1:167491/91‑1 (MQ=255) aaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACAtt > 2:2813191/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc > 2:2304556/1‑91 (MQ=255) aaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc < 2:2061108/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAttttta < 2:2640356/91‑5 (MQ=37) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat > 2:797617/1‑91 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:1299161/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 2:394027/91‑1 (MQ=255) cATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:1959651/91‑1 (MQ=255) ttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAAtata < 2:2456935/91‑1 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg < 1:1609379/91‑1 (MQ=255) tatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAg > 2:2180004/1‑91 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGAc > 1:3008060/1‑91 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGAc > 1:3249616/1‑91 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa < 2:615156/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 1:277496/91‑1 (MQ=255) ttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaa < 2:1498660/91‑1 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACGTTCAATATAGACAAAGt > 1:3328899/1‑91 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGt > 1:69127/1‑91 (MQ=255) tAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGt > 2:178052/1‑91 (MQ=255) aTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt < 2:2257654/91‑1 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 2:857054/1‑91 (MQ=255) tAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt < 1:1522430/91‑1 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:2455496/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg < 2:3613596/91‑1 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg > 1:1284991/1‑91 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTg < 2:1442526/91‑1 (MQ=255) gATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGa > 2:2904036/1‑91 (MQ=255) ctctGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatat < 2:553568/91‑1 (MQ=255) tGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtt > 1:1832906/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 2:2800684/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:3431053/91‑1 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt < 2:160299/91‑1 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1153114/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:1423407/1‑91 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATACAtttt < 2:2647041/91‑1 (MQ=255) cTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTtta > 2:3154797/1‑91 (MQ=255) cTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTtta > 2:71045/1‑91 (MQ=255) atatatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttatt < 2:326673/91‑1 (MQ=255) tatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg > 1:1572396/1‑91 (MQ=255) atTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGa < 1:2691648/91‑1 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 1:218960/1‑91 (MQ=255) gagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtgt < 1:482939/91‑1 (MQ=255) gagGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtgt < 2:1572102/91‑1 (MQ=255) ggTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACa > 2:3579190/1‑54 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:1391462/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:3192474/1‑91 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaaaaa > 1:830992/1‑91 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg < 1:3586035/91‑1 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 2:320087/1‑91 (MQ=255) gTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTg > 1:1642322/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATAtttt > 1:298478/1‑68 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATtg > 2:3723331/1‑78 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 2:1138357/1‑91 (MQ=255) aTTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAAc > 2:3625779/1‑91 (MQ=255) ttAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 1:1341622/1‑91 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa > 2:3473726/1‑91 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 2:492091/91‑1 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 1:3640599/91‑1 (MQ=255) attgaaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa > 1:1855552/5‑91 (MQ=37) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 2:1374103/91‑1 (MQ=255) aaaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATaa < 2:2970495/91‑1 (MQ=255) aaaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg > 1:2538327/1‑91 (MQ=255) aaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAgg < 1:2393345/91‑1 (MQ=255) aaaTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAgg > 1:391108/1‑91 (MQ=255) aaTGTTTTCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGa > 1:1192540/1‑91 (MQ=38) aTGTTTTTATTTATATTAAAATATTTAATATTGACAAATTTTTGTTTATATATATATTTTATTATGATTGTGTAAAAGTTAACATAATGAt < 2:2522888/91‑1 (MQ=255) gttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt > 1:3698687/3‑91 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt < 1:2896850/91‑1 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAttt < 2:3529578/91‑1 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTttat < 2:2569839/59‑1 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc < 2:213050/91‑1 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc < 1:1396785/91‑1 (MQ=255) ttCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:727387/1‑91 (MQ=255) ttCATATAAATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:545450/1‑91 (MQ=255) cATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCt > 1:2571462/1‑91 (MQ=255) aTTTATATGAAAACATTCAATATAGTCAAAATATTGACAACATATATATTTTAATATGATTTTGAAAAAGTAAACATAAGGATTTTCCCtt < 2:3552099/91‑1 (MQ=255) aTTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCtt > 1:1700133/1‑91 (MQ=255) ataaatGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat > 1:2921064/5‑91 (MQ=255) tataTGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttatt < 1:524606/91‑1 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTGTTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattta < 2:2999158/91‑1 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattta < 2:3479829/91‑1 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattta < 2:3692916/91‑1 (MQ=255) atGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttatttat < 1:3753506/91‑1 (MQ=255) tGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATg > 1:2208373/1‑91 (MQ=255) aaaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGaa < 1:3554157/91‑1 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 1:1861254/91‑1 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 2:2571462/91‑1 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 1:2495361/91‑1 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 2:2024223/91‑1 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg > 1:906493/1‑91 (MQ=255) aaaCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 1:1029078/91‑1 (MQ=255) aCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTg > 2:356344/1‑91 (MQ=255) aCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTg < 2:2266079/91‑1 (MQ=255) | TCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTG > USA300TCH1516_ALE/2509703‑2509882 |
| 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: ‑ |