| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,455,699 | A→T | 12.7% | H406L (CAT→CTT) | lyrA → | Lysostaphin resistance protein A |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,455,699 | 0 | A | T | 12.7% | 143.9 / 10.1 | 47 | H406L (CAT→CTT) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base A (19/22); new base T (2/4); total (21/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.78e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 | |||||||||||
CAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCT > USA300TCH1516_ALE/2455561‑2455835 | cagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACata > 1:760639/1‑141 (MQ=255)cagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACata > 1:28584/1‑141 (MQ=255) aaTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGCAAAATAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCg < 1:411151/141‑1 (MQ=255) aTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGa < 2:79666/141‑1 (MQ=255) aTCAGTTAAACAAGCACCACAAAGGGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGa < 1:627025/141‑1 (MQ=255) tCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGa‑a < 2:296558/141‑1 (MQ=255) gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGa‑aaaa > 1:424356/1‑141 (MQ=255) aaaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACt > 1:399024/1‑141 (MQ=255) aaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTg < 2:70125/141‑1 (MQ=255) cAAGCACCACAAAATGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGA‑AAAAACTgaag < 2:11754/141‑1 (MQ=255) gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTgaagaa > 2:121378/1‑141 (MQ=255) caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAAc > 1:65691/1‑141 (MQ=255) caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAAc > 1:54719/1‑141 (MQ=255) gACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGAt < 1:303660/141‑1 (MQ=255) aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATa > 1:153990/1‑141 (MQ=255) tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATaaaaa < 1:293660/141‑1 (MQ=255) tAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACa < 1:561549/141‑1 (MQ=255) cAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAaat < 1:266030/141‑1 (MQ=255) ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGA‑AAAACCTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa < 1:416367/141‑1 (MQ=255) aaaTGAAGATGAAATAGAGCAATCATTAAAAGAAGCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg > 2:270947/1‑141 (MQ=255) gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc < 2:173962/141‑1 (MQ=255) aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt > 1:777211/1‑141 (MQ=255) aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt > 1:777212/1‑141 (MQ=255) cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa < 2:147226/141‑1 (MQ=255) tAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCCAGTACCTCTTAAAAAgat < 2:102101/141‑1 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga > 2:236452/1‑141 (MQ=255) aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTa > 2:95685/1‑141 (MQ=255) ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg > 2:48763/1‑141 (MQ=255) cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc < 1:769394/141‑1 (MQ=255) cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 1:202544/141‑1 (MQ=255) tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa > 1:454328/1‑141 (MQ=255) gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 1:278888/141‑1 (MQ=255) ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCttt > 1:519966/1‑141 (MQ=255) agaagaCAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctat > 1:131554/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatac < 1:593053/141‑1 (MQ=255) acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat > 1:319524/1‑141 (MQ=255) agacGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactata > 2:296480/1‑141 (MQ=255) cGTTCATCAATTGTCATTACTCAAGAAAACCATATAGACAAAAACTCAAGAAAAACCTTCACATCACCACAAACCCAAACAACGCGCTTGCTAGTACCTCTTACAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata < 1:590647/141‑1 (MQ=255) catcaGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATattatt < 1:278351/141‑1 (MQ=255) atcaGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttt < 1:465087/141‑1 (MQ=255) tcaGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt > 1:90045/1‑141 (MQ=255) gTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaa > 1:145953/1‑141 (MQ=255) tGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt > 1:251728/1‑141 (MQ=255) gATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTa > 1:368901/1‑141 (MQ=255) gATGCA‑AAAAAATTATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTaa < 1:274967/141‑1 (MQ=255) aTGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTaa < 2:114624/141‑1 (MQ=255) aGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATCCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACAcc < 2:256504/141‑1 (MQ=255) aaaCATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCctct < 1:667352/141‑1 (MQ=255) aaaCATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCctct < 1:554718/141‑1 (MQ=255) | CAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGA‑AAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCT > USA300TCH1516_ALE/2455561‑2455835 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |