| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,783,168 | T→A | 5.6% | intergenic (‑73/+274) | arcA_2 ← / ← argR_3 | Arginine deiminase/Arginine repressor |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,783,168 | 0 | T | A | 5.6% | 315.5 / 7.7 | 90 | intergenic (‑73/+274) | arcA_2/argR_3 | Arginine deiminase/Arginine repressor |
| Reads supporting (aligned to +/- strand): ref base T (45/40); new base A (3/2); total (48/42) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01 | |||||||||||
AATTGGACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTGGGTC > USA300TCH1516_ALE/2783078‑2783257 | aaTTGGACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTatat > 1:1572318/1‑91 (MQ=255) tGGACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTca < 1:3073004/91‑1 (MQ=255) tGGACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGAATATAATca < 1:400395/91‑1 (MQ=255) gACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTcaca < 1:2144166/91‑1 (MQ=255) gACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTcaca < 1:298530/91‑1 (MQ=255) gACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGAATATAATcaca < 1:1024497/91‑1 (MQ=255) aCCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACAt > 1:3053728/1‑91 (MQ=255) ccATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATa > 1:2016668/1‑91 (MQ=255) cATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaa > 1:2355235/1‑91 (MQ=255) tGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaa < 1:1927268/91‑1 (MQ=255) gatctGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaa < 1:2212840/87‑1 (MQ=255) gTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaa < 1:2500569/91‑1 (MQ=255) tCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaag > 1:553080/1‑91 (MQ=255) tCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaag > 1:1880460/1‑91 (MQ=255) tCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaag < 1:2903978/91‑1 (MQ=255) tCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaag < 1:3036729/91‑1 (MQ=255) tCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATaaagaaag > 1:3083788/1‑91 (MQ=255) cATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGt < 1:2800840/91‑1 (MQ=255) aTGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTc < 1:3521182/91‑1 (MQ=255) tGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCg > 1:3180462/1‑91 (MQ=255) gTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGa > 1:2723773/1‑91 (MQ=255) gTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGa < 1:249089/91‑1 (MQ=255) tATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGaaaa > 1:3143468/1‑91 (MQ=255) aTTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAAt > 1:2243847/1‑91 (MQ=255) tttCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAAtt > 1:759753/1‑91 (MQ=255) tcctccTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTc < 1:3141440/91‑1 (MQ=255) ctcctTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCat > 1:3806184/1‑91 (MQ=255) ctcctTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCat < 1:1240499/91‑1 (MQ=255) tcctTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCata > 1:3664743/1‑91 (MQ=255) cctTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCatat < 1:2464740/91‑1 (MQ=255) tttATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCtt < 1:1253969/91‑1 (MQ=255) tttATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCtt < 1:1222752/91‑1 (MQ=255) tttATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCtt < 1:1222443/91‑1 (MQ=255) ttATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCttt < 1:4014380/91‑1 (MQ=255) aTCTTTGAATTCATTTAGAGTATAGACAATCGTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAGTTTCATATCttttt > 1:3741956/1‑91 (MQ=255) tCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTg > 1:1394503/1‑91 (MQ=255) ttGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTta < 1:788587/91‑1 (MQ=255) ttGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTta > 1:3590762/1‑91 (MQ=255) ttGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTta < 1:594385/91‑1 (MQ=255) tGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTtat < 1:2418825/91‑1 (MQ=255) aaTTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatac < 1:779733/91‑1 (MQ=255) aTTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTataca > 1:693735/1‑91 (MQ=255) aTTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTataca > 1:693722/1‑91 (MQ=255) aTTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTataca > 1:465682/1‑91 (MQ=255) ttCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatacaa > 1:3799197/1‑91 (MQ=255) cATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatacaata > 1:2716656/1‑91 (MQ=255) cATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatacaata > 1:2716697/1‑91 (MQ=255) cATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatacaata < 1:4088491/91‑1 (MQ=255) tttAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTatacaataca > 1:2662958/1‑91 (MQ=255) gagTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACataat > 1:280733/1‑91 (MQ=255) gagTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACataat > 1:2559180/1‑91 (MQ=255) gTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACAtaataa < 1:2687821/91‑1 (MQ=255) gTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACAtaataa < 1:2687787/91‑1 (MQ=255) gTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACAtaataa < 1:1599246/91‑1 (MQ=255) ataGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATg < 1:3667314/91‑1 (MQ=255) ataGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATg < 1:3668364/91‑1 (MQ=255) ataGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATg < 1:1434514/91‑1 (MQ=255) taGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATgg > 1:2405294/1‑91 (MQ=255) taGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATgg > 1:415336/1‑91 (MQ=255) taGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATgg > 1:2405346/1‑91 (MQ=255) aCAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGAtt > 1:3538277/1‑91 (MQ=255) cAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGAttt > 1:1541158/1‑91 (MQ=255) cAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGAttt > 1:2449492/1‑91 (MQ=255) cAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGAttt < 1:372380/91‑1 (MQ=255) aaTCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGAtttt > 1:2334391/1‑91 (MQ=255) tCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTta < 1:1608785/91‑1 (MQ=255) tCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTta < 1:3463461/91‑1 (MQ=255) tCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTta < 1:346721/91‑1 (MQ=255) cTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTtat > 1:202398/1‑91 (MQ=255) aaaCGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACat > 1:3999506/1‑91 (MQ=255) aaaCGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACat > 1:88252/1‑91 (MQ=255) cGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACataaa > 1:2687815/1‑91 (MQ=255) cGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACataaa > 1:2687814/1‑91 (MQ=255) tACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACAtaaataaa > 1:3703509/1‑91 (MQ=255) tACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACAtaaataaa > 1:3671209/1‑91 (MQ=255) tACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACAtaaataaa < 1:4084814/91‑1 (MQ=255) ttaTGTGAATATAATCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAg > 1:1471306/3‑91 (MQ=255) aCATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAg < 1:1117470/91‑1 (MQ=255) cATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAgg > 1:2175726/1‑91 (MQ=255) aTGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGc > 1:3446897/1‑91 (MQ=255) aTGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGc < 1:1750107/91‑1 (MQ=255) aTGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGc > 1:1775826/1‑91 (MQ=255) tgtgAATATAATCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCa > 1:3737321/1‑91 (MQ=255) gtgATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAt < 1:1722127/91‑1 (MQ=255) gtgAATATAATCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAt > 1:3619928/1‑91 (MQ=255) tgATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAtt < 1:2128986/91‑1 (MQ=255) tgATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAtt > 1:1133404/1‑91 (MQ=255) gATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAttt < 1:700095/91‑1 (MQ=255) aTTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAtttt > 1:4153876/1‑91 (MQ=255) aTTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCAtttt > 1:1517798/1‑91 (MQ=255) tataTTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTgg < 1:701659/91‑1 (MQ=255) atatTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTggg < 1:1814961/91‑1 (MQ=255) atatTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTggg < 1:55325/91‑1 (MQ=255) tatTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTGGGt > 1:2673474/1‑91 (MQ=255) atTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTGGGTc > 1:1535901/1‑91 (MQ=255) | AATTGGACCATCTGTCATGTCTATTTCCTCCTTTTATCTTTGAATTCATTTAGAGTATAGACAATCTTCAAACGCTTACATGTGATTATATTCACATAAAGAAAGTCGAAAATTTCATATCTTTTTGTTATACAATACATAATAATGGATTTTTATACATAAATAAAGGCATTTTGGGTC > USA300TCH1516_ALE/2783078‑2783257 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |