| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | 89.0% | intergenic (‑45/+126) | cspA_2 ← / ← USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,440,085 | 0 | G | T | 89.0% | 138.6 / 11.7 | 67 | intergenic (‑45/+126) | cspA_2/USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (2/5); new base T (21/36); total (24/43) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.33e-01 | |||||||||||
TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAAT > USA300TCH1516_ALE/1439948‑1440219 | tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat < 1:860531/141‑1 (MQ=255) aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa < 2:13669/141‑1 (MQ=255) aaTATACGAATACATCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGCTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAc < 1:88442/141‑1 (MQ=255) tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAACATTCATTCAATATGCTTATTCTCATATTACaa > 1:177092/1‑141 (MQ=255) gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa > 2:225058/1‑141 (MQ=255) ttcGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATCTGCTTCTTCTTATATTACAATTAATACa < 2:96387/139‑1 (MQ=255) cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg > 1:328704/1‑141 (MQ=255) tttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTGGTTTCATAATCTGAAACCTCCAAGACTAAATTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAtt < 2:266960/141‑1 (MQ=255) ccTTCAACTTCAATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACt < 2:676442/141‑1 (MQ=255) ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTTTACCTTGTTTCATAATCTTAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa < 1:141486/141‑1 (MQ=255) cAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAACAAATACATGCAAATTTCACTCaaa < 2:47019/141‑1 (MQ=255) cAACGTCGATAAAGCCGAATCCTTTGTCAGCGTTAAACCATTTATCTGTGCCGTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCgaa < 2:447236/141‑1 (MQ=255) acctccGATACTGCCCAATCCTTTTTCAGCGTTAAACCATTTACCTGTACCTTGTCTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAACAAATACATGCAAATTTCACTCAAat < 1:78907/136‑1 (MQ=255) aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCCAat < 2:933332/141‑1 (MQ=255) aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCACTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat < 2:848863/141‑1 (MQ=255) cTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAatat < 1:197319/141‑1 (MQ=255) ttCGAAAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTCCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt < 1:972597/141‑1 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTCATCTTTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt > 1:1051179/1‑141 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTAACTCAAATATTCtt > 2:550723/1‑141 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCCCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt > 1:763622/1‑141 (MQ=255) gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATCTTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat > 1:242999/1‑141 (MQ=255) gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaaa > 1:46985/1‑140 (MQ=255) gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat > 1:495726/1‑141 (MQ=255) gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat > 1:47131/1‑141 (MQ=255) aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCGAAGACTAAAATTCATTCAATATGCTTATTCTCCTATTACAAAAAATACATGCAAATTTCCCTCAAATATTCTTTGCAATATGGa > 2:194683/1‑141 (MQ=255) aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGa < 1:1033296/141‑1 (MQ=255) cTTTTTCAGCGGTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATAGTCTTTGCAATATGGaata < 2:879051/141‑1 (MQ=255) ttgatCAGCGTCAAACCATTTAACTGTACCTTGCTGCATATTCTTAAACTTCCAACATGAAAATTTATTCAATATGCTTATTCTCATAGTACAAAAAATACATGCAAATTTCACTCAAAGATTCTTTGCAATATGGaataa < 2:294994/137‑1 (MQ=255) cttttCAGCGTTAAACCATTTAACTGTTCCTTGTTTCATAATCTGAAACCTCCAAGACTAAACTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa < 2:37003/140‑1 (MQ=255) ttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACGAAAATTCATTCAATATGCTTAATACCATTTTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat < 1:201248/141‑1 (MQ=255) tCAGCGTTAACCCATTTAACTGTACCGTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTTATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat < 2:923032/141‑1 (MQ=255) tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat > 1:998306/1‑141 (MQ=255) gCGTTAAACCATTTAACTGTACCTTCTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg < 2:920521/141‑1 (MQ=255) ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCTAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt < 1:727374/141‑1 (MQ=255) ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTCATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt < 2:405172/141‑1 (MQ=255) aaacccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTa < 2:571568/137‑1 (MQ=255) aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCTATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATCTTCTTTGCAATATGAAATAATCATCTGCTTAAc > 2:163760/1‑141 (MQ=255) aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAAc > 2:163506/1‑141 (MQ=255) aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAGTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt < 2:436289/141‑1 (MQ=255) aaCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCCCTCTATTATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta < 2:584877/141‑1 (MQ=255) aaCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta < 2:1016441/141‑1 (MQ=255) gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttt > 2:64065/1‑140 (MQ=255) tttCATAGTCCGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat > 1:662083/1‑141 (MQ=255) ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATAATCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 1:68267/141‑1 (MQ=255) ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 2:1007090/141‑1 (MQ=255) aaTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTACACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTATATTATAGTGCAGTTATTACCaa > 2:169129/1‑141 (MQ=255) tCTGAAACCTCCAAGACTAAAATTCAATCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAt > 2:659424/1‑141 (MQ=255) tGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTg < 2:221087/141‑1 (MQ=255) gAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc > 2:497280/1‑141 (MQ=255) aacccTCCAAGACTAAAAATCACTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGca < 2:1040338/138‑1 (MQ=255) cTCCGAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTCTATTATAGTGCAGTTATTACCAAATTGcaatac > 1:720333/1‑141 (MQ=255) cTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTTAAATATTCTTTGCAATATGGAATAATCATCTGCTTAATTTGTATTGTAGTGCGGTTATTACCAATTTGgaatta > 2:810018/1‑139 (MQ=255) ccAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTACCTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaa > 1:406700/1‑141 (MQ=255) aCTGAAATTCATGCAATATGCTTATAAGAATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAgtgata < 2:973309/141‑1 (MQ=255) cTAAAATTCTTTTAACATGTGTATTCTCATATTACAAAAAATACATTCAAATTTCACTCAAATATTCTTTGCAATATGTAATAATTATCTGCTTAACTTGTATTGTAGTGCAGTTATTTCCAAATTGCAATACAAtaataa < 2:296087/141‑1 (MQ=255) cTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAAtaataa < 2:324555/141‑1 (MQ=255) cTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAACATCGAATACTCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAAtaataa < 2:850657/141‑1 (MQ=255) tAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaa < 2:244032/141‑1 (MQ=255) aaacTTCATTCAATATGCTTATTCTCAAATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa < 1:981231/141‑1 (MQ=255) aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa < 1:1030789/141‑1 (MQ=255) ttcattcaATATGCTTATTATCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAata < 1:982267/141‑1 (MQ=255) tcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAatat < 1:225058/141‑1 (MQ=255) ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTCTTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa > 1:609847/1‑141 (MQ=255) ttcaATATGCTTATTAGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGACATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa < 1:141355/141‑1 (MQ=255) atatGCTTATTCTCATATTAAAAAAAATACATGCAACTTTCACTCACATATTCTTTGCAATATGTAATAATCATCTGCTTAACTTGTATTATAGTGTAGTTATTTCCAAATTGCAATACAATAATAAAACATATTCATTTa > 1:262662/1‑141 (MQ=255) cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCaa < 1:429950/141‑1 (MQ=255) ttATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAat < 2:328704/141‑1 (MQ=255) | TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAAT > USA300TCH1516_ALE/1439948‑1440219 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |