| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,455,698 | 0 | C | A | 77.8% | 153.9 / 47.1 | 63 | coding (1216/1260 nt) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (22/27); minor base . (9/5); total (31/32) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.37e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01 | |||||||||||
| * | USA300TCH1516_ALE | 2,455,699 | 0 | A | T | 95.2% | 177.8 / ‑4.3 | 64 | H406L (CAT→CTT) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/3); new base T (31/29); total (31/33) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.38e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
TTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA > USA300TCH1516_ALE/2455570‑2455826 || ttAAACAAACATCACAAAGTGGCCAATTAACAAATGATGCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTAATGCAAAAAAAAATATCg < 2:80886/135‑1 (MQ=255) aCAAGCACCACAAAGTTACCATTTAACAAACGATTCAAAAGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATTCA‑AAAAAATTATCGaaaaa < 1:356226/135‑1 (MQ=255) aCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaaaaa < 1:112169/135‑1 (MQ=255) aCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaa > 2:389099/1‑135 (MQ=255) aCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaa > 1:455959/1‑135 (MQ=255) aCAAGCACCACAAAGTGACGAATTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaaa > 1:242420/1‑135 (MQ=255) gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAA‑TTATCGAAAAAACTga > 1:204743/1‑135 (MQ=255) accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaa > 1:82224/1‑135 (MQ=255) tcacaATGTGATGATGAAACAAACGATTCAAGTGTAGATGAAATAGAGCAAGCATTAAAAGAACCTGCGACGTATAAAGAAGACAGACGTTCATCATTTTTAATTGATGCA‑AAAAAATTTTCGTAAATACTgaag < 2:82227/134‑1 (MQ=255) acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGACAAAACTgaagaa > 2:38932/1‑135 (MQ=255) acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTAACGAAAAAACTgaagaa > 2:279171/1‑135 (MQ=255) aaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATTGAAAAAACTGAAGAACaa < 1:22861/135‑1 (MQ=255) aaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACaa > 1:672745/1‑135 (MQ=255) aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAAt < 1:40463/135‑1 (MQ=255) aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAAAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAAt > 1:666582/1‑135 (MQ=255) tgccGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTAAAGAACAATCt > 1:593897/4‑135 (MQ=255) tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCt > 1:497132/1‑135 (MQ=255) tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCt < 1:168279/135‑1 (MQ=255) cGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa > 1:646169/1‑135 (MQ=255) aTTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGa > 2:600153/1‑135 (MQ=255) aTTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCTACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACaaaga < 1:610605/135‑3 (MQ=255) tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAATACAGACGGTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaataat < 2:156387/135‑1 (MQ=255) aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAAGAATAAc > 2:615457/1‑135 (MQ=255) tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCTAAAAATCTGTAGAACAATTTTCAGATAAAAACAAATAATAACAAAGCGCt < 1:9343/135‑1 (MQ=255) aaTCATTAAAAGAACCGGCGACTTATAAATAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACct < 2:480103/135‑1 (MQ=255) tctttAAAAGAACCTGCGACTTATAAAGAAAACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct < 2:35615/132‑1 (MQ=255) tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGATGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACcact > 2:400576/1‑135 (MQ=255) tCATGAAAAGAACCTGCTACTTCTAAAGAAGACAGACGTTAATCAGGTCTAATTGATGCA‑AAAAAATTAACGAAAAAACTGAAGAATAATCTTCAGATAAAAACAAATAGTAACAAAGCGCTTGCTAGTACctct < 2:350166/135‑1 (MQ=255) cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCtt > 2:573350/1‑135 (MQ=255) cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAGTAACAAAGCGCTCGCTAGCACCTCtt > 2:388377/1‑135 (MQ=255) cATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCCCATGCTAGTACCTCtt > 2:141048/1‑135 (MQ=255) tAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCATGCTAGTACCTCTTaaa > 2:265828/1‑135 (MQ=255) aaaGAACCTGCGACTTATAGAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTaaaaa > 2:157476/1‑135 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAGAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa > 2:470133/1‑135 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTacaaa > 2:300521/1‑135 (MQ=255) aaaGAACCTGCGACATATAAAGCAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAAAAAAAAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa < 2:123871/135‑1 (MQ=255) aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg > 2:389654/1‑135 (MQ=255) aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat < 2:204743/135‑1 (MQ=255) gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat < 2:175406/135‑1 (MQ=255) atccTGCGACTTATCAAGAAGACAGATGTTCATCAGCTGTAACTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAATGCGCTTGCTAGTCCCTATTAAAAAgatg < 1:428839/133‑1 (MQ=255) aaCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCATATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg < 2:544164/135‑1 (MQ=255) aaCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTCGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACACAGCGCTTGCTAGTACCTCTTAAAAAgatg < 2:372562/135‑1 (MQ=255) aaCCTGCGACTTAAAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACTAATCGCTTTTTAGTACCTCTTAAAAAgatg < 1:491885/135‑1 (MQ=255) aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga < 1:96766/135‑1 (MQ=255) gctaCTTATAAAGACGACAGACGGTCATCAGTTGTAA‑ACCCAAAAACAAAAAAATCGAAAAAACCGAAGAACAATCTTCAGATAAAAACAAATAAGAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt < 2:429063/132‑1 (MQ=255) cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTa > 2:465952/1‑135 (MQ=255) cTTATAAAGAAGAGAGACGTTCATCAGTTGTAATTTATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATTTCAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 1:525442/135‑1 (MQ=255) ttATAAAGAAGCCAGACGTTCATCAGTTGTAATTTATGCA‑AAAAAATTATCGAAAAATCTGAAGAACAATCTTCAGATAAAAACAAATAATAACTAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 1:81105/135‑1 (MQ=255) ttATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa > 1:100725/1‑135 (MQ=255) taAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACACAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg < 2:638918/135‑1 (MQ=255) aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAGATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc < 1:342078/135‑1 (MQ=255) aggaagtCAGACGTTCATCAGTTGTAATTGAGGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt < 2:338484/133‑1 (MQ=255) acgaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt > 2:45911/3‑135 (MQ=255) gaccgacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTct > 1:188919/1‑135 (MQ=255) aggcGTTCATCAGTTGGAATTGATGCA‑AAAAAATTATCGAAAAAACTGAATAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCACGCGCTTTTctata < 2:227803/132‑1 (MQ=255) agacGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAATAACAATCTTCAGATACATACAAATAATAACTGTGGGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCTTTTctata < 1:129565/135‑1 (MQ=255) acGTTCATCAGTTTTACTGGATGCA‑AAAAAAGTATCGCAAAAACTGAAGAACAAGCTTCAGATAAAAACAAATAGTAACAGAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCCGCGCTTTTctatact < 2:398185/135‑1 (MQ=255) acGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTCGAATGCGCCTTTctatact > 2:582107/1‑135 (MQ=255) cGTTCATCAGTCGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatacta < 2:82224/135‑1 (MQ=255) ttCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactata > 1:421432/1‑135 (MQ=255) catctGTTGTAATTAATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatatc > 1:202630/1‑134 (MQ=255) catcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata > 1:434669/1‑135 (MQ=255) tGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaa < 1:600153/135‑1 (MQ=255) aaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTa < 1:515777/134‑1 (MQ=255) || TTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA > USA300TCH1516_ALE/2455570‑2455826 |
| 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: ‑ |