| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 41,166 | G→A | 9.8% | intergenic (‑33/‑67) | pbp ← / → mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 41,166 | 0 | G | A | 9.8% | 770.5 / 51.4 | 255 | intergenic (‑33/‑67) | pbp/mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
| Reads supporting (aligned to +/- strand): ref base G (129/101); new base A (8/17); total (137/118) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.31e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01 | |||||||||||
Only 100 of 273 total aligned reads displayed.
TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTT > USA300TCH1516_ALE/41076‑41255 | taCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTgtag > 2:3205568/1‑91 (MQ=255) aCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACAAATgtagt < 1:987349/91‑1 (MQ=255) aCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCATTTTCATCAATATACTCCTTATATAAGACTACATTTgtagt < 1:3362483/91‑1 (MQ=255) ccAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTTTTTTTTTTTTCAATATACTCCTTATATAAGACTACATTTgtagta > 2:2521339/1‑91 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATAtt < 1:2552464/91‑1 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 2:831933/91‑3 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 2:1881491/91‑3 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTa > 2:655140/1‑91 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta < 1:893978/91‑4 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta < 2:111109/91‑4 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta < 1:2463398/91‑4 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACCACATTTGTAGTATATTAc > 1:1783279/1‑91 (MQ=255) cGACAACTACAACTATTAAGATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACa < 2:1502379/91‑1 (MQ=255) cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACa > 1:824332/1‑91 (MQ=255) cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACa < 1:1987729/91‑1 (MQ=255) gACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCCTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaa > 2:3524931/1‑91 (MQ=255) acaactacaactATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaa < 1:921007/91‑1 (MQ=255) acaactacaactATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaa > 2:2029167/1‑91 (MQ=255) acaactacaactATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaa < 1:1674943/91‑1 (MQ=255) aactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATg > 2:3102152/1‑91 (MQ=255) aactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATg < 2:898369/91‑1 (MQ=255) ctacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgta > 2:1773165/1‑91 (MQ=255) tacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgtag < 2:2685730/91‑1 (MQ=255) acaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgcagt > 1:3493590/1‑91 (MQ=255) aactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAt < 1:62697/91‑1 (MQ=255) aactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAt > 2:3466940/1‑91 (MQ=255) aactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATACACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAt > 1:1120054/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt > 2:1180352/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt < 1:2089709/91‑1 (MQ=255) aaaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCa > 2:2076830/1‑91 (MQ=255) aaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCaa < 1:53501/91‑1 (MQ=255) gTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaataa > 1:284195/1‑91 (MQ=255) gAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt > 1:2450317/1‑91 (MQ=255) gAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt < 1:3321678/91‑1 (MQ=255) aaCAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGtt < 1:2332038/91‑1 (MQ=255) cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:3425335/91‑1 (MQ=255) cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:774489/91‑1 (MQ=255) aaTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtata > 2:2752898/1‑91 (MQ=255) aTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTATATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATaa < 2:3419083/91‑1 (MQ=255) tttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAt > 1:1416833/1‑91 (MQ=255) ttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtt > 1:459186/1‑91 (MQ=255) tttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttt > 1:102623/1‑91 (MQ=255) ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTGTAAtttt > 2:1974146/1‑91 (MQ=255) ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtttt > 2:86621/1‑91 (MQ=255) ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtttt > 1:1861568/1‑91 (MQ=255) tATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTTTAAttttt > 2:2580757/1‑91 (MQ=255) tATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttttt < 1:33030/91‑1 (MQ=255) aTCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtg > 1:1090288/1‑91 (MQ=255) tCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtgt < 2:1861493/91‑1 (MQ=255) cTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtgtg > 2:158819/1‑91 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat > 2:2327799/1‑91 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat < 1:1233980/91‑1 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat > 2:393724/1‑91 (MQ=255) tgttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat > 1:175713/3‑91 (MQ=255) tcatcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATg < 1:2626389/91‑1 (MQ=255) tcatcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATg < 1:3468014/91‑1 (MQ=255) tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg > 1:562026/1‑91 (MQ=255) caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg > 1:3843407/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt < 2:1762592/91‑1 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt < 2:223078/91‑1 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATAGTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt < 2:3062976/91‑1 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg > 2:3349642/1‑91 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg < 2:2852499/91‑1 (MQ=255) taCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg < 1:2642933/91‑1 (MQ=255) aCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa < 2:1310835/91‑1 (MQ=255) aCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGa < 2:2180797/91‑1 (MQ=255) tatataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgtgt < 1:2238974/91‑1 (MQ=255) tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgtgtat < 2:354204/91‑3 (MQ=255) tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa > 2:1672347/1‑91 (MQ=255) ataAGACTACATTTGTAGTCTATTACACATGTAGTATTTCTGTCAAAATAATGTTCTACTTTTTGTGATATGGAGGTGTAGAAGGTGTTat > 1:1554897/1‑91 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat > 1:2737052/1‑91 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat > 1:120710/1‑91 (MQ=255) taAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatc < 2:2284665/91‑1 (MQ=255) taAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatc < 1:3627372/91‑1 (MQ=255) taAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatc > 1:1689662/1‑91 (MQ=255) aaGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatca > 1:3027139/1‑91 (MQ=255) aaGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatca > 1:1868320/1‑91 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc < 2:2435955/91‑1 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc > 1:135117/1‑91 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc > 1:3152688/1‑91 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc > 1:3525474/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 2:813121/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 1:1615443/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 2:548575/1‑91 (MQ=255) cTACATTTGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt > 2:50325/1‑91 (MQ=255) cTACATTTGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt > 2:2360006/1‑91 (MQ=255) aCATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttt < 1:6631/91‑1 (MQ=255) aCATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttt > 2:3726775/1‑91 (MQ=255) caaatGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 1:3384331/5‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt < 1:93486/91‑1 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 2:1274897/1‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 2:1371944/1‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt < 1:280748/91‑1 (MQ=255) aTTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttttt < 1:2492779/91‑1 (MQ=255) tttGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa > 2:2373276/1‑91 (MQ=255) ttGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa > 2:1033127/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:3836433/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:2390728/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:1480645/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt < 2:2670965/91‑1 (MQ=255) | TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTT > USA300TCH1516_ALE/41076‑41255 |
| 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: ‑ |