Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | USA300TCH1516_ALE | 2,509,785 | T→A | 10.2% | intergenic (‑97/‑273) | narT ← / → USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | USA300TCH1516_ALE | 2,509,785 | 0 | T | A | 10.2% | 158.9 / 7.8 | 49 | intergenic (‑97/‑273) | narT/USA300HOU_RS12920 | putative nitrate transporter NarT/hypothetical protein |
Reads supporting (aligned to +/- strand): ref base T (26/18); new base A (2/3); total (28/21) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 6.39e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
TTTGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACTT > USA300TCH1516_ALE/2509649‑2509925 | tttGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGa < 1:355212/141‑1 (MQ=255) ttGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaa < 2:96665/141‑1 (MQ=255) tgtaatgtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCTTTTATATGaaa > 1:434719/1‑141 (MQ=255) atgtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAt < 1:324213/141‑1 (MQ=255) gtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCACCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc > 2:195884/1‑141 (MQ=255) aaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCaa > 1:489882/1‑141 (MQ=255) aGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAttttta < 2:334023/141‑5 (MQ=255) aGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat < 1:120062/141‑1 (MQ=255) gTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAtttttaa < 1:633990/141‑6 (MQ=255) ccACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaaa > 1:137131/1‑141 (MQ=255) ccACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaaa > 1:137241/1‑141 (MQ=255) cACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg > 1:519017/1‑141 (MQ=255) cTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt > 2:23953/1‑141 (MQ=255) ttttgttttgTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt > 1:128168/1‑141 (MQ=255) ttttgttttgTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt < 1:84928/141‑1 (MQ=255) ttttgtACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTa > 1:559018/1‑141 (MQ=255) aCATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatata > 1:715857/1‑141 (MQ=255) tACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatatat < 1:774020/141‑1 (MQ=255) ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg > 1:565246/1‑141 (MQ=255) tcatcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt > 1:715359/1‑141 (MQ=255) aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTAAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa > 1:313556/1‑141 (MQ=255) tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa > 2:215906/1‑141 (MQ=255) tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa > 1:633739/1‑141 (MQ=255) tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa > 1:693795/1‑141 (MQ=255) ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt > 2:16465/1‑141 (MQ=255) tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa < 1:239318/141‑1 (MQ=255) tttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg > 1:219344/1‑141 (MQ=255) tttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg < 2:313541/141‑1 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAt < 1:688290/141‑1 (MQ=255) aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAt > 2:333558/1‑141 (MQ=255) aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt < 1:516771/141‑1 (MQ=255) atatCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc > 1:500522/1‑141 (MQ=255) aaTACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat > 1:643122/1‑141 (MQ=255) tACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattt < 1:451011/141‑1 (MQ=255) gCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg < 2:152751/141‑1 (MQ=255) ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGt > 1:380133/1‑141 (MQ=255) atatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGAttt > 1:580702/1‑141 (MQ=255) tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTAccc > 1:94484/1‑141 (MQ=255) cAATGTTATTTAAAAACTCTTTCATTTATATTAAAACATTCAATAAAGACAAAGTAATGACGACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACaa < 1:663528/141‑1 (MQ=255) aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAAt < 1:513156/141‑1 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTa > 1:770905/1‑141 (MQ=255) tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTa < 2:151625/141‑1 (MQ=255) aTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATg < 1:281795/141‑1 (MQ=255) aTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATg < 2:266271/141‑1 (MQ=255) gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCt < 1:754804/141‑1 (MQ=255) ttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCtt > 1:176525/2‑141 (MQ=255) cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCtt > 1:142038/1‑141 (MQ=255) tttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCttt > 2:222741/1‑141 (MQ=255) tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTa < 1:385391/141‑1 (MQ=255) atatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACt > 2:305370/1‑141 (MQ=255) tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACtt > 1:395213/1‑141 (MQ=255) | TTTGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACTT > USA300TCH1516_ALE/2509649‑2509925 |
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: ‑ |