| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,064,253 | Δ1 bp | 100% | coding (236/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,064,253 | 0 | C | . | 95.6% | 186.1 / ‑1.1 | 43 | coding (236/1218 nt) | ywtF | Putative transcriptional regulator YwtF |
| Reads supporting (aligned to +/- strand): ref base C (0/1); major base . (21/20); minor base T (0/1); total (21/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
GGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGA > USA300TCH1516_ALE/1064114‑1064385 | ggTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTc > 1:237989/1‑140 (MQ=255) gTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATGTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTct < 1:253829/140‑2 (MQ=255) tAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTctt > 1:638730/1‑138 (MQ=255) tAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTctt < 1:372991/140‑3 (MQ=255) aTCTTATCGTAATAGCCAACTTTATGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCtttt < 1:425309/140‑1 (MQ=255) aTAGTCAACTTTAGGAATGTAGCTTATAGTATCACGTGGAATACTAAGCATTCTAATTTTATTTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTcc < 1:90307/140‑1 (MQ=255) cAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATAATAAGCCTTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTATAATCAAAGCGGCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGt < 1:443411/140‑1 (MQ=255) aaCTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGtt > 1:745298/1‑140 (MQ=255) tAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTatcat > 1:83629/1‑140 (MQ=255) ggAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTCTTTCTTCTTCCATCGTTATCATCg < 1:489128/140‑1 (MQ=255) ggAATGTAGCTGATAGTATCACGTGGAATACTAAGCATACTACTTTGATGTTTTGATTGATTAAAAGTAGTTAAAATAGTAGCGTATGATATCGAGAGTTAAGAATACTGT‑CTTTTTTTCTTGTTCCATCGTTATCATCg > 1:466489/1‑140 (MQ=255) tGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAGAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTATTCTTCCATCGTTATTAGAGATACCTaaga > 1:99676/1‑140 (MQ=255) gATAGTATCATGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaa < 1:567975/140‑1 (MQ=255) gATAGTATCAAGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaa < 1:358653/140‑1 (MQ=255) aTAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAAAGAGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaataaa > 1:5182/1‑140 (MQ=255) tATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTaagaaaagaa > 1:446665/1‑140 (MQ=255) gTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAgaga < 1:123659/140‑1 (MQ=255) ggAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATa > 1:107429/1‑140 (MQ=255) tACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGGGGGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt < 1:676074/140‑1 (MQ=255) tACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt < 1:575748/140‑1 (MQ=255) tACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt < 1:575738/140‑1 (MQ=255) tACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTATTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGgtt < 1:722267/140‑1 (MQ=255) aaGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGttc > 1:511708/1‑140 (MQ=255) aaGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGAGTCAGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTAATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGttc > 1:636289/1‑140 (MQ=255) tCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTGTTCCATCGTTATCATCGATACCAAAGAAAAGAATAGAGATAGGTTGTTCTTCggg > 1:362426/1‑140 (MQ=255) tCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCggg > 1:22752/1‑140 (MQ=255) tttGATTCTTTAATTGATTAAAGGTATTGAAAATCATAGCGTCTGATCTAGAGTGTTAATTATCCT‑TTCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGa < 1:204734/140‑1 (MQ=255) tGATGTTTTGATTGTTTAAAAGTAGTTAATATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACt < 1:117233/140‑1 (MQ=255) tGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACt < 1:574293/140‑1 (MQ=255) aTGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACttt > 1:29961/1‑140 (MQ=255) tGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTtta < 1:205975/140‑1 (MQ=255) tttGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTttatta < 1:761336/140‑1 (MQ=255) agtagtTAAAATCAGAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAAAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGa > 1:399886/1‑140 (MQ=255) gtagtTAATATCATAGCGTCTGATCTAGAGTGTTCCTCATCCTGT‑TTTTTTTTTTTCTTCCATCGTTATCATGGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGAt < 1:237554/140‑1 (MQ=255) gtagtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGAt < 1:700761/140‑1 (MQ=255) gtTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGa > 1:661574/1‑140 (MQ=255) aaTCATAGCGTCTGGTCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGAtt < 1:477520/140‑1 (MQ=255) aaTCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGAtt > 1:608184/1‑140 (MQ=255) tCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTGTCTTCTTCCATCGTTATCATCGATACCCAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTACGTTGGATTGACGATTAg > 1:523185/1‑140 (MQ=255) tAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATTTTCGTTACTTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAt < 1:251804/140‑1 (MQ=255) tAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAt > 1:449918/1‑140 (MQ=255) tAGCGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAt > 1:649331/1‑140 (MQ=255) cGTCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCAtttt < 1:712460/140‑1 (MQ=255) tCTGATCTAGAGTGTTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTg < 1:432423/140‑1 (MQ=255) gtTCAGCATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGagaag > 1:630949/1‑140 (MQ=255) cATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGa > 1:644978/1‑140 (MQ=255) cATCCTGT‑CTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGa > 1:543000/1‑140 (MQ=255) | GGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTTTTTCTTCTTCCATCGTTATCATCGATACCTAAGAAAAGAATAGAGATAGGTTGTTCTTCGGGATTGACTTTATTATCTCTTAAGTTGGATTGACGATTAGCATTTTTGCTGTCTTGAGAAGATTCGA > USA300TCH1516_ALE/1064114‑1064385 |
| 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: ‑ |