| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 41,171 | T→C | 8.3% | intergenic (‑38/‑62) | 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 | 41,171 | 0 | T | C | 8.3% | 753.4 / 44.0 | 252 | intergenic (‑38/‑62) | pbp/mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
| Reads supporting (aligned to +/- strand): ref base T (133/97); new base C (12/9); total (145/107) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01 | |||||||||||
Only 100 of 269 total aligned reads displayed.
AACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTAT > USA300TCH1516_ALE/41081‑41261 | aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTatat > 2:49041/1‑91 (MQ=255)aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTatat > 1:229416/1‑91 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATAtt < 1:2552464/91‑1 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTa < 2:3777506/91‑1 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACCACATTTGTAGTATATTAc > 1:1783064/1‑91 (MQ=255) cGACAACTACAACTATTAAGATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACa < 2:1502379/91‑1 (MQ=255) cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACa < 1:822900/91‑1 (MQ=255) gACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaa < 2:2114205/91‑1 (MQ=255) acaactacaactATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaa < 1:921007/91‑1 (MQ=255) acaactacaactATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaa < 1:1674943/91‑1 (MQ=255) caactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAAt > 2:3287159/1‑91 (MQ=255) aactacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATg < 2:2809953/91‑1 (MQ=255) actacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgt > 1:1561063/1‑91 (MQ=255) ctacaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgta < 1:1223368/91‑1 (MQ=255) acaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgtagt > 2:93486/1‑91 (MQ=255) acaactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgcagt > 1:3493590/1‑91 (MQ=255) aactaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAt > 2:3466940/1‑91 (MQ=255) actaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAtt < 1:3696028/91‑1 (MQ=255) actaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAtt > 2:3534192/1‑91 (MQ=255) actaTTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTAtt > 1:236837/1‑91 (MQ=255) ttAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATg > 1:3866989/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt > 2:1180352/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt > 2:3104675/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt > 1:2620936/1‑91 (MQ=255) aaaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCa < 1:2424727/91‑1 (MQ=255) aaaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCa > 1:117136/1‑91 (MQ=255) aaTAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCaa < 1:957488/91‑1 (MQ=255) gAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt > 1:2450462/1‑91 (MQ=255) aCAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTta < 2:3499455/91‑1 (MQ=255) aCAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTta < 1:655140/91‑1 (MQ=255) cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:2250468/91‑1 (MQ=255) cAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:774489/91‑1 (MQ=255) aaTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtata > 2:2752898/1‑91 (MQ=255) aaTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtata > 2:1766748/1‑91 (MQ=255) aTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTATATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATaa < 2:3419083/91‑1 (MQ=255) aTTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGAAGTATTTATGTCAAAATAATGTTATaa < 2:1053909/91‑1 (MQ=255) tttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAt > 1:1416833/1‑91 (MQ=255) ttttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtt > 1:2020455/1‑91 (MQ=255) tttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTCTTTATGTCAAAATAATGTTATAAttt < 2:2215265/91‑1 (MQ=255) tttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttt < 1:3378823/91‑1 (MQ=255) tttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttt > 1:102623/1‑91 (MQ=255) ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTGTAAtttt > 2:1974146/1‑91 (MQ=255) ttATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtttt > 1:1861643/1‑91 (MQ=255) tATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTTTAAttttt > 2:2580757/1‑91 (MQ=255) aTCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtg > 1:1090288/1‑91 (MQ=255) tCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtgt < 2:1861493/91‑1 (MQ=255) tttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGa < 1:2783966/91‑1 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat > 2:2327799/1‑91 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGat < 1:1233980/91‑1 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGGGat > 1:175299/1‑91 (MQ=255) tttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGata > 1:56094/1‑91 (MQ=255) tcatcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATg < 1:3468014/91‑1 (MQ=255) tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg > 1:562443/1‑91 (MQ=255) caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg > 2:2994820/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt < 2:1762592/91‑1 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt > 1:876853/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt > 1:179818/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATAGTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt < 2:3062976/91‑1 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg > 2:3349642/1‑91 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg < 1:51490/91‑1 (MQ=255) tataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtgt < 1:2234481/91‑1 (MQ=255) taCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg < 1:2642933/91‑1 (MQ=255) cTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGaa > 1:331284/1‑91 (MQ=255) cTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGaa < 2:1920145/91‑1 (MQ=255) cTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGaa > 2:2698117/1‑91 (MQ=255) tCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAg > 2:867643/1‑91 (MQ=255) ccgtatataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATGTGTGTGATATGGAGGTGTAGAAgg < 2:1554897/88‑1 (MQ=255) cTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt > 2:638116/1‑91 (MQ=255) atataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGtt < 2:2555768/91‑1 (MQ=255) tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa > 2:1672347/1‑91 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat < 2:836559/91‑1 (MQ=255) taAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatc > 1:1689661/1‑91 (MQ=255) aaGGCTGCACTTGTAGTATATTATGCAGGTAGTAGTTGTGTCACAATTTTGTGTTGATGGTTGTGATATGGAGGTGTAGAAAGTGTTataa < 2:1344733/91‑3 (MQ=255) aaGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatca > 1:3027139/1‑91 (MQ=255) aGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcat > 1:2825664/1‑91 (MQ=255) gACTACATTTGTAGTATATTACAACTGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc < 2:3601077/91‑1 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc < 2:2435793/91‑1 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc < 1:1870804/91‑1 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc > 1:3525474/1‑91 (MQ=255) gACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcatc > 1:3152688/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 2:548575/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 2:813121/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 1:3292163/1‑91 (MQ=255) aCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCt > 1:1615443/1‑91 (MQ=255) cTACATTTGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt > 1:1413961/1‑91 (MQ=255) tACATTTGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttt > 2:207623/1‑91 (MQ=255) caaatGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 1:3384331/5‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 2:1274502/1‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt < 1:93486/91‑1 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt < 2:236837/91‑1 (MQ=255) aTTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttttt < 1:2492779/91‑1 (MQ=255) tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa < 1:1264531/91‑1 (MQ=255) tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa > 2:2358126/1‑91 (MQ=255) ttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa > 2:3437070/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:1480645/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt < 2:2670965/91‑1 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:3836433/1‑91 (MQ=255) atatTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAg > 2:1376059/1‑91 (MQ=255) tatTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGt < 1:281193/91‑1 (MQ=255) ttACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGtat > 1:3548713/1‑91 (MQ=255) | AACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTAAGTAT > USA300TCH1516_ALE/41081‑41261 |
| 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: ‑ |