Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | USA300TCH1516_ALE | 2,372,419 | C→T | 11.1% | intergenic (+170/+22) | USA300TCH1516_02262 → / ← pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | USA300TCH1516_ALE | 2,372,419 | 0 | C | T | 11.1% | 152.5 / 9.3 | 54 | intergenic (+170/+22) | USA300TCH1516_02262/pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
Reads supporting (aligned to +/- strand): ref base C (26/22); new base T (3/3); total (29/25) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
GAAGAAACACGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCAC > USA300TCH1516_ALE/2372284‑2372559 | gaagaaACACGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTGCCAATGATTGGTAGTCg < 1:522514/141‑1 (MQ=255) agaaACACGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTGCCAATGATTGGTAGTCG‑tt < 1:639852/141‑1 (MQ=255) agaaACACGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTGCCAATGATTGGTAGTCG‑tt < 2:245598/141‑1 (MQ=255) acacGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATATTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑tttttt < 1:401104/141‑1 (MQ=255) gTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTgtgt > 1:169497/1‑141 (MQ=255) ccAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCt > 2:159972/1‑141 (MQ=255) caacaaTTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTg < 1:176727/141‑1 (MQ=255) caacaaTTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATAACGCTTTCTGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTg < 1:666814/141‑1 (MQ=255) aaTTTTAAAAGAAGTANATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGAtt > 1:778144/1‑141 (MQ=255) aTTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGAttt > 1:25122/1‑141 (MQ=255) aaaaGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCa > 1:562027/1‑141 (MQ=255) aaaGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCAt < 1:556624/141‑1 (MQ=255) agaagTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGa > 1:310274/1‑141 (MQ=255) aagTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAAc < 1:558078/141‑1 (MQ=255) tatTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAata < 1:396721/141‑1 (MQ=255) tttATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATg > 1:128379/1‑141 (MQ=255) atCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTa < 2:232631/141‑1 (MQ=255) atCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTa < 1:65706/141‑1 (MQ=255) tCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTag < 1:746898/141‑2 (MQ=255) tCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTAc > 1:699672/1‑141 (MQ=255) ggATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAg < 2:316687/141‑1 (MQ=255) cATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTAcc > 2:254244/1‑141 (MQ=255) ttCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCAt < 1:260106/141‑1 (MQ=255) tCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAatacata > 1:115400/1‑141 (MQ=255) cGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAatacatac < 2:93200/141‑1 (MQ=255) tttATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACAtt > 2:176027/1‑141 (MQ=255) tttATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTAAAGAATGAATAGTAACATTAATACATACAtt > 1:631031/1‑141 (MQ=255) ttATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGa < 1:215940/141‑1 (MQ=255) cttcttATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTActtc > 1:499554/1‑141 (MQ=255) ttcttATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTActtct > 2:62531/1‑141 (MQ=255) tcttATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTActtctt < 2:151139/141‑1 (MQ=255) ttATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGttt < 1:60976/141‑1 (MQ=255) ttACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTaga > 1:487849/1‑141 (MQ=255) cTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGAt < 2:60953/141‑1 (MQ=255) aGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGTATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCAt > 1:373250/1‑141 (MQ=255) aaaaaCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTa > 2:86826/1‑141 (MQ=255) aaaaaCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTa > 1:215379/1‑141 (MQ=255) aaaaCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTaa > 1:505178/1‑141 (MQ=255) aaaCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACATAATGAATAGTACCATTAATACATACAATATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCTTTGTAAt < 1:624240/141‑1 (MQ=255) aaCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAAtt > 1:396396/1‑141 (MQ=255) aCGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTg > 1:729389/1‑141 (MQ=255) cGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTgg < 1:355448/141‑1 (MQ=255) cGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTgg > 1:321002/1‑141 (MQ=255) gACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGa < 1:515985/141‑1 (MQ=255) gACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGa > 1:31466/1‑141 (MQ=255) cTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATa < 1:80624/141‑1 (MQ=255) aCCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAAACATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATCGGATAGa < 1:624407/141‑1 (MQ=255) cAATCATTTGCACTCG‑TTTTTTGTGTCTGTATTTAACCATAAACAAAAATAAAGGACAAAATTAATAGTACCATTAATACATACATTATCGTATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGaaa < 1:195215/141‑1 (MQ=255) cAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGaaa > 2:73765/1‑141 (MQ=255) aatgaTTGGTAGTCGTTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGaaa > 2:17037/5‑141 (MQ=255) tgaTTGGTAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGNaaata > 1:69103/3‑141 (MQ=255) tCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaata > 1:459117/1‑141 (MQ=255) gaTTGGTAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaataa > 2:289179/2‑141 (MQ=255) ggCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATTAATAGTACCATTATTACATACATTATCGGTTGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATcc > 1:277071/1‑141 (MQ=255) cAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCcac > 1:694749/1‑141 (MQ=255) | GAAGAAACACGTCCAACAATTTTAAAAGAAGTATATTTATATCGGATATTTAAAGACATTCATAATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCG‑TTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCAC > USA300TCH1516_ALE/2372284‑2372559 |
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |