| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 308,137 | A→C | 5.4% | I129L (ATT→CTT) | lytR_1 → | Sensory transduction protein LytR |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 308,137 | 0 | A | C | 5.4% | 297.6 / 3.3 | 86 | I129L (ATT→CTT) | lytR_1 | Sensory transduction protein LytR |
| Reads supporting (aligned to +/- strand): ref base A (43/38); new base C (3/2); total (46/40) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
ATTTTGAAACCGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAATATTATTG > USA300TCH1516_ALE/308047‑308227 | atTTTGAAACCGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCaa > 1:1195308/1‑91 (MQ=255) tttGAAACCGTTTGGGCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAATTGCACtt < 1:259716/91‑1 (MQ=255) aaCCGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGaa < 1:1294955/91‑1 (MQ=255) ccGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATg > 1:3444480/1‑91 (MQ=255) cGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGa > 1:1909837/1‑91 (MQ=255) ttGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGatat < 1:686636/91‑1 (MQ=255) tGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATg > 1:211384/1‑91 (MQ=255) gTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTc < 1:3705100/91‑1 (MQ=255) tCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCg > 1:3819386/1‑91 (MQ=255) tCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCg < 1:3758203/91‑1 (MQ=255) tCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCg > 1:2944220/1‑91 (MQ=255) tCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCg > 1:2943662/1‑91 (MQ=255) aaaaCGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCg < 1:738590/91‑1 (MQ=255) aaaaCGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCg > 1:2828424/1‑91 (MQ=255) gTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAttt > 1:1024885/1‑91 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt > 1:1008846/1‑91 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt > 1:2480077/1‑91 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt > 1:2480064/1‑91 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt < 1:2207614/91‑1 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt > 1:1971947/1‑91 (MQ=255) tATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAAtttt > 1:954028/1‑91 (MQ=255) aTTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTg < 1:2493114/91‑1 (MQ=255) aTTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTg > 1:3886057/1‑91 (MQ=255) ttGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGa > 1:2874445/1‑91 (MQ=255) ttGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGa > 1:1275803/1‑91 (MQ=255) ttGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGa > 1:1823856/1‑91 (MQ=255) gAACAAGCATTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATc > 1:1235931/1‑91 (MQ=255) gAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATc < 1:3831994/91‑1 (MQ=255) cAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCaaa < 1:684859/91‑1 (MQ=255) cAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCaaa < 1:687019/91‑1 (MQ=255) gCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCt > 1:1666915/1‑91 (MQ=255) gCAGTCAATAAAGTGAGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATTAAAGCt > 1:2050432/1‑91 (MQ=255) aGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTa > 1:2971658/1‑91 (MQ=255) tCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTAcc > 1:1451158/1‑91 (MQ=255) tCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTAcc < 1:3472912/91‑1 (MQ=255) tCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTAcc > 1:1097659/1‑91 (MQ=255) tCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTAcc > 1:1451075/1‑91 (MQ=255) tCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAAGAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTAcc < 1:1146064/91‑1 (MQ=255) aaTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTg < 1:2240480/91‑1 (MQ=255) aaTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTg < 1:2240647/91‑1 (MQ=255) aaTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTg > 1:3913503/1‑91 (MQ=255) aaTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTg > 1:1725565/1‑91 (MQ=255) aTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGt < 1:1046223/91‑1 (MQ=255) aTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGt > 1:1105272/1‑91 (MQ=255) aTAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGt < 1:509304/91‑1 (MQ=255) tAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGtt < 1:3064142/91‑1 (MQ=255) aaaGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTg < 1:3951064/91‑1 (MQ=255) aaGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGa < 1:3180094/91‑1 (MQ=255) tgcgtgcgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAAt > 1:2166373/1‑91 (MQ=255) cgtgcgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTg > 1:2369086/1‑91 (MQ=255) cgtgcgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTg > 1:3247874/1‑91 (MQ=255) gcgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACg < 1:1710607/91‑1 (MQ=255) cgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGa < 1:1936081/91‑1 (MQ=255) cgACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGa < 1:1936425/91‑1 (MQ=255) aaGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAAt < 1:796658/91‑1 (MQ=255) aGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAAtt < 1:3008910/91‑1 (MQ=255) gCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTc < 1:845228/91‑1 (MQ=255) gCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTc > 1:3483839/1‑91 (MQ=255) aaaGATGATAATAACGCAAGTGCAATTGCTAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTcaca < 1:3325132/91‑1 (MQ=255) aaaGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTcaca > 1:2269958/1‑91 (MQ=255) aaaGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTcaca < 1:3736432/91‑1 (MQ=255) aaGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACAt < 1:559167/91‑1 (MQ=255) aGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATg < 1:2670561/91‑1 (MQ=255) atgatAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGtt > 1:4036096/1‑91 (MQ=255) atgatAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGtt > 1:1387256/1‑91 (MQ=255) atgatAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGtt > 1:1630703/1‑91 (MQ=255) cattcGCAATTGCACTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGca > 1:3081922/5‑91 (MQ=255) ttcGCAATTGCACTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGcaac > 1:2143232/3‑91 (MQ=255) aaCGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGcaac < 1:413506/91‑1 (MQ=255) cGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGcaacaa < 1:1027472/91‑1 (MQ=255) gCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACaaa < 1:201384/91‑1 (MQ=255) gCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACaaa > 1:1028835/1‑91 (MQ=255) cAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACaaaa > 1:1274097/1‑91 (MQ=255) cAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACaaaa > 1:1274170/1‑91 (MQ=255) aaGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAat < 1:106736/91‑1 (MQ=255) aaGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAat > 1:2486026/1‑91 (MQ=255) aaGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAat < 1:106461/91‑1 (MQ=255) aGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAata > 1:3278328/1‑91 (MQ=255) gTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAatat < 1:1274623/91‑1 (MQ=255) tGCACTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt < 1:3450397/91‑1 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt < 1:535566/91‑1 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt > 1:3048084/1‑91 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt < 1:321316/91‑1 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt > 1:480377/1‑91 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt < 1:375470/91‑1 (MQ=255) tGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatt > 1:1445341/1‑91 (MQ=255) gCACTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAAtatta > 1:737240/1‑91 (MQ=255) aTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAATATTATTg > 1:1673170/1‑91 (MQ=255) aTTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAATATTATTg > 1:2674979/1‑91 (MQ=255) | ATTTTGAAACCGTTTGGTCAAAAACGTATTGAACAAGCAGTCAATAAAGTGCGTGCGACTAAAGCCAAAGATGATAATAACGCAAGTGCAATTGCGAATGATATGTCGGCGAATTTTGATCAAAGCTTACCTGTTGAAATTGACGATAAAATTCACATGTTAAAGCAACAAAATATTATTG > USA300TCH1516_ALE/308047‑308227 |
| 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: ‑ |