| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,517,775 | A→C | 12.9% | S953A (TCA→GCA) | narG ← | Respiratory nitrate reductase 1 alpha chain |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,517,775 | 0 | A | C | 12.9% | 259.7 / 32.0 | 85 | S953A (TCA→GCA) | narG | Respiratory nitrate reductase 1 alpha chain |
| Reads supporting (aligned to +/- strand): ref base A (35/39); new base C (2/9); total (37/48) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.03e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01 | |||||||||||
TTCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCACTCCAC > USA300TCH1516_ALE/2517686‑2517863 | ttCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGaa > 1:2755680/1‑91 (MQ=255)ttCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGaa > 1:2486821/1‑91 (MQ=255)ttCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGaa > 1:2485636/1‑91 (MQ=255)ttCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGaa < 1:3958951/91‑1 (MQ=255) tCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGaaa < 1:263126/91‑1 (MQ=255) gCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATa < 1:3785299/91‑1 (MQ=255) gCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATa > 1:2387421/1‑91 (MQ=255) tAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACt < 1:2348836/91‑1 (MQ=255) aGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACtt < 1:570165/91‑1 (MQ=255) aGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACtt < 1:1894754/91‑1 (MQ=255) gAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTa > 1:956886/1‑91 (MQ=255) gAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTa < 1:979664/91‑1 (MQ=255) gAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTa < 1:2622331/91‑1 (MQ=255) gAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTa < 1:1551151/91‑1 (MQ=255) gAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTa > 1:957386/1‑91 (MQ=255) aaTATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGt < 1:2115649/91‑1 (MQ=255) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTAttt < 1:793147/91‑2 (MQ=38) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTAttt < 1:352812/91‑2 (MQ=38) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTAttt < 1:3878642/91‑2 (MQ=38) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGCAATACTAAGTAttt < 1:726307/91‑2 (MQ=255) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGCAATACTAAGTAttt < 1:727744/91‑2 (MQ=255) tCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTg > 1:99037/1‑91 (MQ=255) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTAtttc < 1:1763005/91‑3 (MQ=38) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGc < 1:3335702/91‑1 (MQ=255) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGc < 1:3336929/91‑1 (MQ=255) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGc > 1:351156/1‑91 (MQ=255) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGc < 1:3597133/91‑1 (MQ=255) cTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGc < 1:2170164/91‑1 (MQ=255) tttAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCAt > 1:3985904/1‑91 (MQ=255) ttAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTATTTCATc < 1:1077541/91‑1 (MQ=37) tAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTATTTCATct < 1:2617053/91‑2 (MQ=37) aaCGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCTGATGCAATACTAAGTATTTCATctg < 1:2218839/91‑3 (MQ=37) aaCGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAg > 1:3672097/1‑91 (MQ=255) aaCGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAg > 1:1753937/1‑91 (MQ=255) aCGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGc < 1:1165600/91‑1 (MQ=255) gCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTAc > 1:237424/1‑91 (MQ=255) aTTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACAt > 1:1013043/1‑91 (MQ=255) ttCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACAtt < 1:489142/91‑1 (MQ=255) ttCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACAtt < 1:3142193/91‑1 (MQ=255) tCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTa > 1:321511/1‑91 (MQ=255) ccAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTAc < 1:3914022/91‑1 (MQ=255) ccAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTAc > 1:4011443/1‑91 (MQ=255) ccAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTAc > 1:1671341/1‑91 (MQ=255) ccAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTAc > 1:435962/1‑91 (MQ=255) ccAGTGTGTTCTTCGAGATCTTCATATGCTTTGTGTGGTAATTTACCATTCGTAGGAGATGAGATACTTAGTATTGCATCAGCTACATTAc < 1:1512040/91‑1 (MQ=255) gTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTg > 1:2350105/1‑91 (MQ=255) ttcttcGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGAGCTGTa < 1:3228351/91‑1 (MQ=255) cttcGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATc > 1:1257022/1‑91 (MQ=255) cGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAAt > 1:949821/1‑91 (MQ=255) gaTCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACg < 1:3692153/91‑1 (MQ=255) gaTCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACg < 1:4130595/91‑1 (MQ=255) tCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTg > 1:1509183/1‑91 (MQ=255) cTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTgg < 1:3192679/91‑1 (MQ=255) cTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACATgg > 1:4123317/1‑91 (MQ=255) ttCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGa > 1:1264026/1‑91 (MQ=255) tCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGAc > 1:1936194/1‑91 (MQ=255) tCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGAc < 1:2279753/91‑1 (MQ=255) cATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACg > 1:3951952/1‑91 (MQ=255) tatGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGAt < 1:1801440/91‑1 (MQ=255) tttttGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGct < 1:1457889/91‑1 (MQ=255) tttttGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGct > 1:4083226/1‑91 (MQ=255) ttttGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGctc > 1:295730/1‑91 (MQ=255) tttGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGctct < 1:1636286/91‑1 (MQ=255) ttGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCtctc < 1:2762562/91‑1 (MQ=255) gtgATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTcac > 1:2627137/1‑91 (MQ=255) gtgATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTcac < 1:3075748/91‑1 (MQ=255) gtgATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTcac > 1:3240924/1‑91 (MQ=255) aTAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGa < 1:2750595/91‑1 (MQ=255) tAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGaa > 1:1499896/1‑91 (MQ=255) aTTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatc < 1:61582/91‑1 (MQ=255) aTTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatc > 1:2919574/1‑91 (MQ=255) ttACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatcat < 1:2364533/91‑1 (MQ=255) ttACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatcat < 1:1327953/91‑1 (MQ=255) ttACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatcat < 1:1430826/91‑1 (MQ=255) ttACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAatcat < 1:337317/91‑1 (MQ=255) aCCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAAtcatca > 1:1384317/1‑91 (MQ=255) cATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCAtt > 1:2903607/1‑91 (MQ=255) ttCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTg > 1:3289135/1‑91 (MQ=255) tCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGt < 1:3788571/91‑1 (MQ=255) tCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGt < 1:3788338/91‑1 (MQ=255) gTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTAt > 1:1614571/1‑91 (MQ=255) gTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTAt > 1:1067422/1‑91 (MQ=255) tAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATc < 1:982417/91‑1 (MQ=255) agctgATGCAATACTAAGTATTTCATCTGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCa > 1:386963/5‑91 (MQ=25) aGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCa > 1:2368966/1‑91 (MQ=255) aGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCa > 1:2176387/1‑91 (MQ=255) gCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGATGATTCGCTCTCACAGAATCATCATTTGTATCAc < 1:2398349/91‑1 (MQ=255) tgATGCAATACTAAGTATTTCATCTGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCACTc > 1:1123239/2‑91 (MQ=37) aTGAAATACTTAGTATTGCATAAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCACTCCa < 1:463508/91‑1 (MQ=255) tGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCACTCCAc < 1:2350683/91‑1 (MQ=255) | TTCGCTAGAAATATCTTTTAACGGCATTCCAGTTTGTTCTTCGAGATCTTCATATGATTTTTGTGATAATTTACCATTCGTAGCAGATGAAATACTTAGTATTGCATCAGCTACATTACGTGCTGTATCAATACGTGGACGATTCGCTCTCACAGAATCATCATTTGTATCACTCCAC > USA300TCH1516_ALE/2517686‑2517863 |
| 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: ‑ |