| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,455,692 | 0 | G | . | 86.7% | 99.0 / 11.6 | 30 | coding (1210/1260 nt) | lyrA | Lysostaphin resistance protein A |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base . (13/13); minor base A (2/2); total (15/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
TCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT > USA300TCH1516_ALE/2455557‑2455825 | tCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaa < 1:41577/141‑1 (MQ=255) gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCCaaaaaa > 2:265718/1‑141 (MQ=255) cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaag < 1:120061/141‑1 (MQ=255) aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa < 1:134458/141‑1 (MQ=255) caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACa > 2:138643/1‑141 (MQ=255) tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt < 2:49282/141‑1 (MQ=255) ggACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAAAAATTAAGAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt < 1:27568/140‑1 (MQ=255) aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATaa > 2:195076/1‑141 (MQ=255) ctaTTAAACAACAGATTCAAATGGAGACGAAAGAGAGCAATCATTAAAAGAACCTGAGACTTACAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGGAGAACAATCTTCAGATaaa < 2:119511/139‑1 (MQ=255) cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg < 1:247716/141‑1 (MQ=255) aaaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc < 1:119010/141‑1 (MQ=255) aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAACAAATA‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGc > 2:320753/1‑141 (MQ=255) gagCAATCATTAATAGAACCTGCGACTTATAAAGAAGACAGACGTGCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAgcatcatc < 2:270533/141‑8 (MQ=255) cAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaa > 1:191168/1‑141 (MQ=255) tAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatg > 2:128580/1‑141 (MQ=255) aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga < 1:150015/141‑1 (MQ=255) aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc > 1:354283/1‑141 (MQ=255) aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATATTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAACCCTTAAAAAGATGATGc > 2:368/1‑141 (MQ=255) gAACCTGGGACGTATAGAGAAGACAGACGTTCATCAGTTGTAAGTGATGCA‑AAAAAAGTATCGAAAAGACTGAAGAACAATGTTCAGATAAAAACAAATAATAGCAGAGCGCTTGCTAGTACCTCTTGAAAAGATGATGCt < 2:352733/141‑1 (MQ=255) aCCTGCGACTTATAAAGAAGACAGACGTCCATTAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg < 1:8217/141‑1 (MQ=255) ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc > 1:238741/1‑141 (MQ=255) ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTCCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc > 1:125752/1‑141 (MQ=255) cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGACGATGCTAGCAAGCGCt < 1:212172/141‑1 (MQ=255) ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt > 2:67898/1‑141 (MQ=255) acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCACTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactac > 1:8574/1‑140 (MQ=255) agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat > 2:118728/1‑141 (MQ=255) acGTTCATCAGTTGTAATTGATGCA‑AACAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat > 1:263157/1‑141 (MQ=255) tcaGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt < 1:138643/141‑1 (MQ=255) caGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc > 1:171336/1‑141 (MQ=255) tGTAATTGATG‑AAAAAAAATTATCGAAAAAACTGAATAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTTGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaa < 2:84742/141‑1 (MQ=255) ttGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt < 2:356822/141‑1 (MQ=255) | TCAGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTT > USA300TCH1516_ALE/2455557‑2455825 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |