| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 9,710 | T→C | 6.9% | intergenic (+15/+72) | gyrA → / ← nnrD | DNA gyrase subunit A/ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 9,710 | 0 | T | C | 6.9% | 146.4 / 4.1 | 59 | intergenic (+15/+72) | gyrA/nnrD | DNA gyrase subunit A/ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase |
| Reads supporting (aligned to +/- strand): ref base T (29/24); new base C (2/2); total (31/28) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.11e-01 | |||||||||||
GGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATAC > USA300TCH1516_ALE/9570‑9848 | ggAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACtt < 2:400733/141‑1 (MQ=255)ggAAATGCAATTCATACTGAAGGGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATAGAGAATAATAAAAAATAAGACtt > 2:267804/1‑141 (MQ=255) aaTGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGAAGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATAAGATGAAGAATAATAAAAAATAAGACATccc > 2:38450/1‑141 (MQ=255) tGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta > 1:189100/1‑141 (MQ=255) tGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta < 2:91551/141‑1 (MQ=255) ggCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta > 2:145611/2‑141 (MQ=255) cAATTTATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata < 1:527923/141‑1 (MQ=255) cAATTCATACTGAAGTGATTGATTCAGAAGAACATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata < 1:12970/141‑1 (MQ=255) cAATTCATACTGAAGTGATTGATTCAGAAAAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTCCCCtaca < 1:8264/141‑3 (MQ=255) aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGCGTTATCTatat > 1:68762/1‑141 (MQ=255) aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAACAATAATAAAAAATAAGACTTCCCTatat > 1:317502/1‑141 (MQ=255) aCTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAgggg > 2:374545/1‑141 (MQ=255) cTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGa < 1:255560/141‑1 (MQ=255) aaGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTCCCCTACATATAGGGAAGTc < 2:327004/141‑1 (MQ=255) tgattgatTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTa > 2:399945/1‑141 (MQ=255) ttgattCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATAATCAGATGAAGACTAATAAAAAATAAGACTTCGCGATATGTAGGGGAGTCGTAttt > 2:401917/1‑141 (MQ=255) attCAGAAGAAAATGATGAAGATGGACGTAGTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTa < 2:479582/141‑1 (MQ=255) ttCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTAATGTGTAt > 1:125918/1‑141 (MQ=255) gaagaaAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTa > 2:247364/1‑141 (MQ=255) aaagaaAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTa < 1:121175/140‑1 (MQ=255) aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt > 2:206278/1‑141 (MQ=255) aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt < 2:196079/141‑1 (MQ=255) aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt < 2:521018/141‑1 (MQ=255) atgatgAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTa < 1:203120/141‑1 (MQ=255) tgatgaAGATGGACGTATTGAAGTGAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTGTTTTTATGCTAGAAAGTaa > 1:358346/1‑141 (MQ=255) tgatgaAGATGGACGGATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTaa > 1:416016/1‑141 (MQ=255) tgatgaAGATGGACGCATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTaa > 1:415945/1‑141 (MQ=255) gatgaAGATGGACGTATTGAAGTAAGACAAGATTTCATTGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAGAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAAt < 1:365030/141‑1 (MQ=255) aGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCttt > 1:2237/1‑141 (MQ=255) gggACGTATTGAAGTAAGACAAGATTTCATGGATCGGGTTGAAGAAGTTAAATAACAATCATCAGATGGAGAATAATAAAAAATAAGACTGCACTATATGTAGGGGAGTCTTATTTTTATGCTACAAAGTAATGCTTTACt < 2:228553/140‑1 (MQ=255) gACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAAAAGACCAGCGACAATCATCAGATGAAGAATAATAAAAAATAAGATTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACtat < 1:181737/141‑1 (MQ=255) aCGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATACGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACtatt > 2:493723/1‑140 (MQ=255) ttGAAGTTAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGTCTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCaa < 1:209252/141‑1 (MQ=255) ttGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCTCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCaa < 1:28895/141‑1 (MQ=255) aGTAAGACTAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGAt < 2:559004/141‑1 (MQ=255) cAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGTTTAGTaaa > 2:508684/1‑140 (MQ=255) cAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAAt > 2:149515/1‑141 (MQ=255) aTTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACt > 1:54491/1‑141 (MQ=255) ggATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTc < 2:7327/141‑1 (MQ=255) cGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAACAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTACTGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAAt < 2:200975/141‑1 (MQ=255) gtTGAAGAAGATATACAACAATCATCAGATGAAAAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGt > 2:93312/1‑141 (MQ=255) aagaagATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCa < 2:420619/141‑1 (MQ=255) agaTATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGc > 1:249310/1‑141 (MQ=255) atatACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTATAATTGTTTAAtaacga > 2:418000/1‑136 (MQ=255) atatACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTAAAGGTAGGGGAGTCTTATGTTTATGCTAGAAAGTAATGCTTTACTATATTCAAGGATTGGACATGACTAACTTTCTAATTGTTTCATTGAGt > 2:393123/1‑141 (MQ=255) acaacaATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTAACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg < 1:374545/141‑1 (MQ=255) caaTCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGAAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTAtt > 2:414783/1‑141 (MQ=255) tcaGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTg > 1:473300/1‑141 (MQ=255) aGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGAt < 1:257800/141‑1 (MQ=255) gATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTTTCCAGATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATa < 1:155296/141‑1 (MQ=255) aaTGAAGAATAATAAAAAATAAGACTGCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATa < 1:450215/140‑1 (MQ=255) ataataAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGa > 1:83238/1‑141 (MQ=255) ataataAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGa < 2:323921/141‑1 (MQ=255) aaTAAGACTCCCCTACATATAGGGAAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGcac > 1:538544/1‑141 (MQ=39) tAAGACTCCCCTACATATAGGGAAGTCTTATTTTTATGCTAGAAAGTACTGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGCcaccc > 2:88078/1‑140 (MQ=38) aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACtt < 2:391247/84‑1 (MQ=255) aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACtt > 1:391247/1‑84 (MQ=255) aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTATAGTTTTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACcaca > 1:526442/1‑141 (MQ=255) aaCTTCCCTACTTGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacat < 1:206122/140‑1 (MQ=255) cTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTTTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatac < 1:224591/141‑1 (MQ=255) cTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacctac > 1:189948/1‑141 (MQ=255) attCCCTAGATGTAGTGGAGTCTTATTTTGATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatac < 2:106738/140‑1 (MQ=255) | GGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATAC > USA300TCH1516_ALE/9570‑9848 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |