| 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 | 90.3% | 81.6 / 3.4 | 31 | coding (1216/1260 nt) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (11/16); minor base . (2/1); total (13/18) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.65e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
| * | USA300TCH1516_ALE | 2,455,699 | 0 | A | T | 100.0% | 94.7 / ‑6.5 | 32 | H406L (CAT→CTT) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base T (13/18); total (13/19) | |||||||||||
| 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. | |||||||||||
ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC > USA300TCH1516_ALE/2455565‑2455831 || accAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaa < 2:166275/139‑1 (MQ=255) aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa < 2:268206/141‑1 (MQ=255) aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa > 1:91967/1‑141 (MQ=255) caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGCAGAACa > 2:332674/1‑141 (MQ=255) gTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGa < 1:58064/141‑1 (MQ=255) tGACTATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt < 1:368645/141‑1 (MQ=255) gACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATa < 1:87077/141‑1 (MQ=255) aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAataata > 1:307108/1‑141 (MQ=255) aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACGATCTTCAGATAAAAACAAATAATAACAAAgc > 1:186263/1‑141 (MQ=255) tGAAGCTGAAATAAAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATA‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCt < 2:150933/141‑1 (MQ=255) tGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcgca > 1:93457/1‑140 (MQ=255) aaaaTGAAATAGAGCAATAATTAAAAGAACCGGCGAATTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTg < 2:135418/138‑1 (MQ=255) aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAACGCGCTTGCTAGTAcc < 1:155564/141‑1 (MQ=255) aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc > 1:246652/1‑141 (MQ=255) agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCtt > 1:310940/1‑141 (MQ=255) aagcATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa < 1:2847/138‑1 (MQ=255) aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACATACGTTCATCCGTTATAATTTATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaa < 1:366188/141‑1 (MQ=255) tgaaaaGAACCCGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCATCAGACAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTACAAAgat < 1:284957/139‑1 (MQ=255) aaaGAACCTGCGACGGATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAATACGTCTTAAAAAgatgat > 2:32288/1‑141 (MQ=255) cTGCGACTTATATATAAGACAGCTCTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACACATAATAACAACGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 2:333580/141‑1 (MQ=255) gACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg < 1:158621/141‑1 (MQ=255) aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc < 1:275586/141‑1 (MQ=255) attATAAAGAAGAGAGACGTACATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt < 2:71328/140‑1 (MQ=255) aagaagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta > 2:120959/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGATAGTCCCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact > 2:141821/1‑141 (MQ=255) acagacGTTCATCAGTTGTAATTGATATA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctaaactaa > 2:80134/1‑140 (MQ=255) acGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat > 1:229182/1‑141 (MQ=255) acGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat < 2:94726/141‑1 (MQ=255) ttCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAGAtattat > 2:232885/1‑141 (MQ=255) atcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTTCCACGTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt < 1:332674/141‑1 (MQ=255) aGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAACAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCt < 2:237513/141‑1 (MQ=255) aaaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTATCAcc < 2:258185/139‑1 (MQ=255) || ATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC > USA300TCH1516_ALE/2455565‑2455831 |
| 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: ‑ |