| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 1,039,559 | G→A | 6.7% | S36S (AGC→AGT) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 1,039,559 | 0 | G | A | 6.7% | 193.4 / 3.3 | 60 | S36S (AGC→AGT) | etk | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| Reads supporting (aligned to +/- strand): ref base G (26/30); new base A (2/2); total (28/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01 | |||||||||||
CGATGAGTTAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAGGCGCT > CP009273/1039415‑1039702 | cGATGAGTTAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACACTGa > 1:183984/1‑149 (MQ=255) aTGAGTTAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGataa < 1:118314/150‑1 (MQ=255) aGTTAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGAtaataa < 1:546852/150‑1 (MQ=255) ttAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAAc < 1:803218/150‑1 (MQ=255) gggATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTa < 1:869572/150‑1 (MQ=255) cATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGt > 2:721771/1‑149 (MQ=255) atatCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTg < 1:859082/149‑1 (MQ=255) gCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCa > 2:677321/1‑150 (MQ=255) ggCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACt < 2:140269/150‑1 (MQ=255) gCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTc < 1:263100/150‑1 (MQ=255) gCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTc < 1:453517/150‑1 (MQ=255) ccGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCg < 2:106034/150‑1 (MQ=255) cGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGc > 2:880764/1‑150 (MQ=255) gCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGcc > 2:63045/1‑150 (MQ=255) agaATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAGCAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGAcc < 2:213838/150‑1 (MQ=255) gaATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCa < 1:353198/150‑1 (MQ=255) aaTGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGAc > 2:368772/1‑147 (MQ=255) tGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGAc < 1:973261/150‑1 (MQ=255) ggCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGAc > 1:543102/1‑149 (MQ=255) gTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACACTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAg > 1:367693/1‑150 (MQ=255) ttGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGGAg > 1:174439/1‑149 (MQ=255) ttGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAg > 2:922508/1‑149 (MQ=255) ccTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAg > 1:881420/1‑145 (MQ=255) tttttGCTTAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAgatcgat < 1:789492/150‑1 (MQ=255) aaCCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTc > 1:456386/1‑150 (MQ=255) aaCCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACACTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTc < 2:367693/150‑1 (MQ=255) ccTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCt < 1:780945/150‑1 (MQ=255) gACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAg < 1:152306/149‑1 (MQ=255) gACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGt > 2:552547/1‑150 (MQ=255) cAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGtgct < 1:63045/150‑1 (MQ=255) gTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCt > 2:892626/1‑150 (MQ=255) ccTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCtggt < 2:383282/146‑1 (MQ=255) cTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCg > 2:395096/1‑149 (MQ=255) gATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTAt > 2:409859/1‑150 (MQ=255) aTAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTAtt > 1:293710/1‑150 (MQ=255) tAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTc < 1:711995/150‑1 (MQ=255) aTTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCata > 1:704222/1‑150 (MQ=255) ggTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATAtt < 2:735656/149‑1 (MQ=255) gtgtGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATAtttt < 2:37245/150‑1 (MQ=255) gtgtGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATAttt < 2:540385/149‑1 (MQ=255) gtgtGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATAttt < 1:815186/149‑1 (MQ=255) tgCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACACTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTa < 2:183984/149‑1 (MQ=255) cTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGtt < 2:13742/150‑1 (MQ=255) ttAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTg > 1:705747/1‑150 (MQ=255) tAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGt > 2:520775/1‑150 (MQ=255) aCAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTc < 2:146459/149‑1 (MQ=255) cGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGt < 1:880764/150‑1 (MQ=255) aGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTAt > 2:586329/1‑150 (MQ=255) tAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTAttt < 2:807038/150‑1 (MQ=255) gCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTtat < 2:944122/150‑1 (MQ=255) gACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGAtctc > 1:264182/1‑90 (MQ=255) aCAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCa < 2:264182/90‑1 (MQ=255) cGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTc > 1:4165/1‑149 (MQ=255) aGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAAtt < 2:293710/149‑1 (MQ=255) aGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTa < 1:395096/150‑1 (MQ=255) aTAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCt > 1:609959/1‑149 (MQ=255) aaCGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAg > 1:36662/1‑150 (MQ=255) aCGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAgg > 1:153135/1‑150 (MQ=255) cgcgGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAGgc > 1:102133/1‑150 (MQ=255) ggTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAGGCGCt > 2:87791/1‑150 (MQ=255) | CGATGAGTTAGGGATCATATCGCTCAGGCCGCTGAGAATGGCGTTGCCCTGTTTTTGCTCAACCTGGACCAGAGTATCTGCCTGATAAATTGGTGTGCTTAACAGCGAGTAAGCGACAGCGATCAGCGTGAATAACGCGGTCACGCTGATAATAAACTTACGGTGATCCCATAACTCGCCGACCAGACGAAGCAGATCGATCTCATTTTCCTGAGTGCTGCCTGGTGGCGTATTCATATTTTTAGTTGTCATCGTATTTTATAAACTCAAATTACCGGCTGAGGCGCT > CP009273/1039415‑1039702 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |