| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | 100% | 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 | 85.4% | 126.5 / 20.2 | 48 | coding (1216/1260 nt) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (25/16); minor base . (4/3); total (29/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01 | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
| * | USA300TCH1516_ALE | 2,455,699 | 0 | A | T | 100.0% | 144.9 / NA | 50 | H406L (CAT→CTT) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (29/21); total (29/21) | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACA > USA300TCH1516_ALE/2455568‑2455829 || aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaa < 2:389097/141‑1 (MQ=255) gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaaa > 1:287199/1‑141 (MQ=255) gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGGTGTAATTGAT‑GCA‑AAAAAATTATCGaaaaaa > 1:139012/1‑141 (MQ=255) aaGCACCACAAAGTGACAATTAAACAAACGATCCAAATGAAAATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGATGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTgaaga < 1:67782/141‑1 (MQ=255) cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACactg > 1:315633/1‑138 (MQ=255) acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAAAAATCt > 1:215551/1‑141 (MQ=255) acaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGGTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCt > 1:115474/1‑141 (MQ=255) aaaGGGACGATTTAACAAACGATTCAAAGGAAGATGAAATAGAGCAATCATTAAAAGAAGCTGCGACGTATAAACAAGACAGACGTACATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAATACTGAAGAACAATCTTc < 2:187576/141‑1 (MQ=255) gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAATAACAATCTTCAGa > 1:40278/1‑141 (MQ=255) cGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCACAAG‑‑ATAATTTATAGTCAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa > 1:389975/1‑141 (MQ=255) gATTTAACAAACTATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGCACAGTCTTCGGATaacc < 2:185135/141‑3 (MQ=255) gATATAACAAACGATTCAAAGGAAGATGAAATAGATCAATCATTAAAAGAACCTGCGACTTATAAACAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa < 2:296809/141‑1 (MQ=255) tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCATAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc > 1:328360/1‑141 (MQ=255) tttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc > 2:13416/1‑141 (MQ=255) ttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACa > 2:55921/1‑141 (MQ=255) aaTGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAGAAAATAACAAAacg > 2:23555/1‑141 (MQ=255) gATGGAATAGAGCAATGATTAAAAGAACCTGCCACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt < 2:220610/141‑1 (MQ=255) aaTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACATAGCGCTTGCt < 2:269846/140‑1 (MQ=255) aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCgctagcta > 2:198057/1‑141 (MQ=255) aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa > 1:385689/1‑141 (MQ=255) aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc > 1:63196/1‑141 (MQ=255) agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc < 2:132066/141‑1 (MQ=255) gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct < 1:376576/141‑1 (MQ=255) aaaaGAACCTGCGACTTATAAAGAATACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga < 2:268367/141‑1 (MQ=255) aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga > 2:301116/1‑141 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTGATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAgatgat > 2:213537/1‑141 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACCATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatgat > 1:255989/1‑141 (MQ=255) aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAAACATCAGATAAAAACAAATAATAACAAAGCACTAGCTAGTACCTCTTAAAAAgataat > 2:15203/1‑141 (MQ=255) aaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTCGCTAGTACGTCTTAAAAAGatgatg > 1:362092/1‑141 (MQ=255) gAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCt > 2:117688/1‑141 (MQ=255) aaaacTGTGACTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTGCAGACAAAAACAAATAATAACAAAGCTCTTGCTAGTACCTCTTAAAAAGATGATGCt < 1:306117/137‑1 (MQ=255) tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 2:386398/141‑1 (MQ=255) tGCGACTTATAAAGAAGACAGACGGTCAACAGTCGTAATTGAT‑TCA‑AAAAAATTATCGAAAAAACTGAAGCACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 1:53345/141‑1 (MQ=255) tGCGACTTAAAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 2:153105/141‑1 (MQ=255) gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg > 1:209057/1‑141 (MQ=255) cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt > 1:248080/1‑141 (MQ=255) cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt > 2:215817/1‑141 (MQ=255) aaaGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAATTGATGCTAGCAAGCGCTTTTct > 1:247040/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAACGCTTTTctattct > 1:16607/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTCTTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact < 1:77216/141‑1 (MQ=255) gacGTTCATCAGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata < 1:329829/141‑1 (MQ=255) cGTTCATCAGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCGAGCGCTTTTCTATACTATAtatt > 1:357012/1‑141 (MQ=255) catcaGTTGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttt > 1:256597/1‑141 (MQ=255) catcaGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACACTCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGGTGCTAGCCAGCGCATTTCTATACTATATATTAttt > 1:111188/1‑141 (MQ=255) attaGTTGTAATTGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATTTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt < 1:86299/138‑1 (MQ=255) atGTAATTGAT‑GCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaa < 2:303790/140‑1 (MQ=255) aaTTGAT‑GCA‑AAAAAATTATCGAAAACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt < 1:3721/141‑1 (MQ=255) tGAT‑GCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTATTAAAAAGATGATGCTAGCAAGCGCTTTTATATAAAATATATTATTTTTATAAAATTTTa > 2:258304/1‑141 (MQ=255) tgcaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAAGAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAaca < 2:139012/137‑1 (MQ=255) agaaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAaca < 2:287199/137‑1 (MQ=255) || AGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGAT‑GCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACA > USA300TCH1516_ALE/2455568‑2455829 |
| 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: ‑ |