| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,582,141 | Δ1 bp | 7.7% | coding (1169/1353 nt) | pnbA → | Para‑nitrobenzyl esterase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,582,141 | 0 | T | . | 7.7% | 294.2 / 17.9 | 91 | coding (1169/1353 nt) | pnbA | Para‑nitrobenzyl esterase |
| Reads supporting (aligned to +/- strand): ref base T (38/45); new base . (2/5); total (41/50) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.56e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01 | |||||||||||
AATATACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGTCGA > USA300TCH1516_ALE/2582053‑2582229 | aaTATACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTc < 1:3568115/91‑1 (MQ=255)aaTATACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTc > 1:3785333/1‑91 (MQ=255) atatACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCatatcta < 1:2495102/91‑4 (MQ=255) atatACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCatatcta < 1:2566711/91‑4 (MQ=255) atatACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCt < 1:2730485/91‑1 (MQ=255) tataCAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCatatctag < 1:443485/91‑5 (MQ=255) taCAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATA‑TCTAG‑aa < 1:830625/91‑2 (MQ=255) taCAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATA‑TCTAG‑aa < 1:1173191/91‑2 (MQ=255) taCAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATA‑TCTAG‑aa < 1:396301/91‑2 (MQ=255) aCAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑at < 1:3054093/91‑1 (MQ=255) aGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATg < 1:916747/91‑1 (MQ=255) aGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATg > 1:3725198/1‑91 (MQ=255) gATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATgg > 1:592482/1‑91 (MQ=255) gATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATA‑TCTAGAATATgg < 1:4004187/91‑1 (MQ=255) gATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATA‑TCTAGAATATgg < 1:3698914/91‑1 (MQ=255) gATTCAAACGCACAACTATGGCTTGCTGAACTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATACTCTAG‑ATATgg > 1:1208637/1‑91 (MQ=255) ttCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTa < 1:2564232/91‑1 (MQ=255) ttCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTa > 1:899852/1‑91 (MQ=255) ttCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTa < 1:3159977/91‑1 (MQ=255) cAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTAtt < 1:2025387/91‑1 (MQ=255) aaaCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTAttt > 1:3592835/1‑91 (MQ=255) aaaCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTAttt > 1:1036423/1‑91 (MQ=255) aaCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTAtttt > 1:2321249/1‑91 (MQ=255) aCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTg > 1:2761017/1‑91 (MQ=255) aCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTg < 1:1454124/91‑1 (MQ=255) aCGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTg < 1:242495/91‑1 (MQ=255) cGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTgg < 1:1236069/91‑1 (MQ=255) acaACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTc < 1:3335322/91‑1 (MQ=255) caACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCg < 1:3715690/91‑1 (MQ=255) aaCTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCgg < 1:607570/91‑1 (MQ=255) aaCTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCgg < 1:2872271/91‑1 (MQ=255) aCTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGa < 1:395596/91‑1 (MQ=255) cTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGaa < 1:4052049/91‑1 (MQ=255) tATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGaaa > 1:2141270/1‑91 (MQ=255) tGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATCTTCTAG‑ATATGGTATTTTGGTTCGGAAACt > 1:1800765/1‑91 (MQ=255) tGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACt < 1:3564765/91‑1 (MQ=255) tGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACt > 1:1800780/1‑91 (MQ=255) gCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTa > 1:3617392/1‑91 (MQ=255) gCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTa > 1:3045104/1‑91 (MQ=255) gCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTa > 1:200663/1‑91 (MQ=255) cTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTAc < 1:1569230/91‑1 (MQ=255) cTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGGTCGGAAACTTAc < 1:3173253/91‑1 (MQ=255) ttGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATGATAG‑ATATGGTATTTTGGTGCGGAAACTcaca > 1:382658/1‑91 (MQ=255) tGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACaa < 1:2731366/91‑1 (MQ=255) tGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACaa < 1:669048/91‑1 (MQ=255) tGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACaa < 1:757171/91‑1 (MQ=255) aaTTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATAtt > 1:2680144/1‑91 (MQ=255) aaTTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATAtt > 1:3916436/1‑91 (MQ=255) aaTTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATAtt < 1:1615094/91‑1 (MQ=255) ttGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTagc > 1:2705481/1‑91 (MQ=255) tGCATGACATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTggca > 1:3221651/1‑91 (MQ=255) gcacggcatgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑AGATGGTATTTTGGTTCGGAAACTTACAAATATTagcag > 1:2386699/1‑91 (MQ=255) tggcatgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCAGAAACTTACAAATATTAGCAGcac > 1:482666/1‑91 (MQ=255) gcatgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACAt < 1:1660002/91‑1 (MQ=255) catgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATc > 1:43013/1‑91 (MQ=255) catgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATc < 1:1075187/91‑1 (MQ=255) catgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATc > 1:42195/1‑91 (MQ=255) tgATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCaa > 1:584362/1‑91 (MQ=255) gATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAat < 1:1591405/91‑1 (MQ=255) aTACTTCTAGCGCACACTATCTCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAata > 1:3743672/1‑91 (MQ=255) tACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAatat > 1:2688256/1‑91 (MQ=255) aCTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATc < 1:2251851/91‑1 (MQ=255) aCTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATc < 1:461136/91‑1 (MQ=255) tCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCcaa > 1:3569500/1‑91 (MQ=255) aGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCcaacaa > 1:3541277/1‑91 (MQ=255) gcACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTg < 1:453516/91‑1 (MQ=255) gcACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTg > 1:1419842/1‑91 (MQ=255) cacaCTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGc < 1:3251691/91‑1 (MQ=255) acacTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCt < 1:2411368/91‑1 (MQ=255) cacTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTc > 1:1095137/1‑91 (MQ=255) cacTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTc > 1:320869/1‑91 (MQ=255) acTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCa > 1:3108690/1‑91 (MQ=255) acTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCa > 1:3935694/1‑91 (MQ=255) tATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCAcc < 1:215851/91‑1 (MQ=255) aTCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCt < 1:2054083/91‑1 (MQ=255) aTCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCt < 1:1106812/91‑1 (MQ=255) aTCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCt < 1:1510520/91‑1 (MQ=255) tCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTCGCAGCACATCAATATCCAACAACTGCTCACCtt > 1:3405687/1‑91 (MQ=255) cGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTa < 1:3125044/91‑1 (MQ=255) cGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTa < 1:2812971/91‑1 (MQ=255) cGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTa < 1:2678372/91‑1 (MQ=255) gCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTaa > 1:1048773/1‑91 (MQ=255) cAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTaaa < 1:3180154/91‑1 (MQ=255) gTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCCACAACTGCTCACCCTAAAtt > 1:1734514/1‑91 (MQ=255) tGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAAttt < 1:1744691/91‑1 (MQ=255) tGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAAttt < 1:2595130/91‑1 (MQ=255) tGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAAttt < 1:1519431/91‑1 (MQ=255) gCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAAtttt > 1:1354795/1‑91 (MQ=255) gCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTCCTCACCTTAAAtttt < 1:2414665/91‑1 (MQ=255) aCCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAg < 1:2963610/91‑1 (MQ=255) aCCATA‑TCTAGAATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAg > 1:2947587/1‑91 (MQ=255) ccATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGt > 1:1037805/1‑91 (MQ=255) ccATA‑TCTAGAATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGt > 1:3708077/1‑91 (MQ=255) cATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGTc < 1:1835006/91‑1 (MQ=255) tatTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGTCGa < 1:1478810/91‑1 (MQ=255) | AATATACAAGATTCAAACGCACAACTATGGCTTGCTGAATTTGCATGGCATGATACTTCTAGCGCACACTATCGCAGTGCTTACCATATTCTAG‑ATATGGTATTTTGGTTCGGAAACTTACAAATATTAGCAGCACATCAATATCCAACAACTGCTCACCTTAAATTTTTAAGTCGA > USA300TCH1516_ALE/2582053‑2582229 |
| 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: ‑ |