| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,433,870 | A→G | 10.7% | D287G (GAC→GGC) | dapA → | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,433,870 | 0 | A | G | 10.7% | 140.6 / 6.3 | 55 | D287G (GAC→GGC) | dapA | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| Reads supporting (aligned to +/- strand): ref base A (28/20); new base G (3/3); total (32/23) | |||||||||||
| 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 | |||||||||||
GTTATCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGCAACAACGC > USA300TCH1516_ALE/1433730‑1434009 | gTTATCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAACCACATGa > 2:510273/1‑141 (MQ=255)gTTATCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGa > 1:396079/1‑141 (MQ=255) ttATCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGac < 2:418646/141‑1 (MQ=255) aTCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGacac < 2:380649/141‑1 (MQ=255) aTCAGCTTTATCAGTTGATAATAACCCACTGCCTATTAAATCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATCACGTCTACCATCGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGacac < 2:901913/141‑1 (MQ=255) tCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGAcaca < 1:864615/141‑1 (MQ=255) tCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGAcaca < 1:25000/141‑1 (MQ=255) aGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACAtt < 2:924406/141‑1 (MQ=255) ttATCAGTTGATATTAACCCAATTCCTATTAACGATCTAACAAGTTATCTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTaaa > 1:222354/1‑141 (MQ=255) atTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAAt > 1:777640/1‑141 (MQ=255) atTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAAt > 1:481617/1‑141 (MQ=255) atTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGAGTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAAt > 2:3905/1‑141 (MQ=255) atTAACCCAATTCCTATTAAAGCTCTAACAAGTTAATTCGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAAt > 1:889995/1‑141 (MQ=255) aaCCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAg > 1:746108/1‑141 (MQ=255) ttAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACt > 1:518453/1‑141 (MQ=255) ttAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACt > 1:702180/1‑141 (MQ=255) ttAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACt > 2:440196/1‑141 (MQ=255) gcttgaaCAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTGCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTg < 2:336987/136‑1 (MQ=255) gCTCTAACAAGTTAGTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTg < 2:725460/141‑1 (MQ=255) tAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTAGCTTTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAGAATATTGCTAATTggttt > 2:620073/1‑138 (MQ=255) tAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTa > 2:360364/1‑141 (MQ=255) tAACAAGTTATACAGGATTTAGAAATCACGAAGCAGGTCTACCATTGGTTAGCCTAGAAGACACAGATACTAAAGTGCTTCGTGAAACATATAACACATTAAAATCGTGTGCAAATGAGTGAAAATATTACTAAtggcata > 2:160122/1‑135 (MQ=255) aCAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGTAAATATTACTAATTGGCTATg < 1:487864/141‑1 (MQ=255) aCAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTAAAAATATTACTAATTGGCTATg > 1:116895/1‑141 (MQ=255) aaGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACAGAGGCAACACCTAAAGCGGGGGAAAATGAGTGAAAATATTACGAAGTGGCtcgggc > 1:306980/1‑136 (MQ=255) gATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAAAAGATACAGATACTAAAGTGCCTCGTGAAACAAATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCa < 2:753124/141‑1 (MQ=255) tttGGAAATTATGAATTACGTCTACCATTTGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAAc < 2:136706/141‑1 (MQ=255) tttGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAAc < 2:937976/141‑1 (MQ=255) tttGGAAATTATGAAGTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAACGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAAc < 1:870624/141‑1 (MQ=255) ggAAATTATGAATTACGTCTACCAGTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAGcgcg < 2:652504/141‑1 (MQ=255) ggAAAGCATGACTTACTGCTAACATTGGTCAGGCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAAcgcg < 2:922536/141‑1 (MQ=255) gAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGGGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGACATGAATCAACGCGt > 2:604675/1‑141 (MQ=255) aTTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGc < 1:594889/141‑1 (MQ=255) tATGAATTACGTCTACCATTGGTTCGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTa > 1:687910/1‑141 (MQ=255) aaTTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGAtt > 1:495599/1‑141 (MQ=255) cGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCag < 1:33316/141‑1 (MQ=255) cGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCag < 1:59973/141‑1 (MQ=255) tCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCagaa < 1:189197/141‑1 (MQ=255) gcTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCagaa < 1:481254/140‑1 (MQ=255) tgaCCATTGGATAGCCTAGAAGATACAGAAACTAAAGGGCTTCGGGAAACATAAGACACATTTAAAGCGGGGGAAAATGAGGGAAAATATAACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCagaag < 2:284240/139‑1 (MQ=255) tACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGGGCAATGAATGAACGCGTTGCAAGGTTAGCggagaa > 1:391037/1‑138 (MQ=255) gCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGa > 1:63902/1‑141 (MQ=255) cTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGaaa > 2:650876/1‑141 (MQ=255) gaagaTACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCg > 1:874543/1‑141 (MQ=255) aagaTACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGt > 1:946350/1‑141 (MQ=255) cagatacTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGGAGAAGAAAAAGGACATGAAATCGTTgggga > 2:597402/1‑140 (MQ=255) cagatacTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGACATCGTTggggg > 1:561053/1‑140 (MQ=255) cTAAGGTGCTGCGGGAAACATATGATACATTTAAAGCGGGTGAAAATGAGTGAAAATACTACTAATTGGCTATGGCGAAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATCGa < 2:268166/141‑1 (MQ=255) aaaGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGaaa > 1:432088/1‑141 (MQ=255) gAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg < 1:440196/141‑1 (MQ=255) gAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg < 2:702180/141‑1 (MQ=255) gAAACATATGGCACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTCGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg < 2:518453/141‑1 (MQ=255) gAAACATATGACACGTTTAAAGCGGGTGCAAATGAGTGAAAATATTACGAATTGGCGAGGGAGCAATGAATCAACGCGTTGCTAGATTAGAGGAAGAAAAAGAACATGAAATCGTTGGGGTCATTGAAAATacacaaacag > 2:201224/1‑135 (MQ=255) gAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGaaaa > 2:927626/1‑140 (MQ=255) gAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg > 1:696252/1‑141 (MQ=255) gAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg > 1:803264/1‑141 (MQ=255) gAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAg > 1:636002/1‑141 (MQ=255) aaaCATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGc < 1:55768/141‑1 (MQ=255) aCATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGcaa > 2:79469/1‑141 (MQ=255) tGACACATTTAAAGCGGGTGAAAATGAGAAACAATATTACTAATTGGCTATGGCGCAATGAATGAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACAGAAAGcaaacacg > 2:9171/1‑136 (MQ=255) aacacATTTAAAGCGGGTGAAAATGAGTGAAAATACTACTAATTGGCTATGGCCCAATGAATCAACGCGTTGCTAGTTGAGCAGAAGAAAAAGGACATGAAAGCGTTCGGGTCATTGAAAATACACCGAAAGCAACAACGc < 2:222354/140‑1 (MQ=255) | GTTATCAGCTTTATCAGTTGATATTAACCCAATTCCTATTAAAGCTCTAACAAGTTATTTAGGATTTGGAAATTATGAATTACGTCTACCATTGGTTAGCCTAGAAGATACAGATACTAAAGTGCTTCGTGAAACATATGACACATTTAAAGCGGGTGAAAATGAGTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAAGAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGCAACAACGC > USA300TCH1516_ALE/1433730‑1434009 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |