| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,679,710 | G→T | 30.1% | G65V (GGC→GTC) | ssaA2_4 → | Staphylococcal secretory antigen ssaA2 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,679,710 | 0 | G | T | 30.1% | 18.0 / 11.3 | 20 | G65V (GGC→GTC) | ssaA2_4 | Staphylococcal secretory antigen ssaA2 |
| Reads supporting (aligned to +/- strand): ref base G (9/5); new base T (4/2); total (13/7) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-01 | |||||||||||
CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC > USA300TCH1516_ALE/2679584‑2679846 | cTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAAt < 2:11355/140‑1 (MQ=255) aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTaa < 2:133223/140‑1 (MQ=255) tCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCaa > 2:153843/1‑140 (MQ=255) gCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCAAAAAATTGGTATTACAATGCACGTAAACCAAAATATg > 2:243773/1‑140 (MQ=255) cATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCAAAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATgg > 2:52475/1‑139 (MQ=255) aTGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGATAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAACCAAAATATGCg > 1:148754/1‑140 (MQ=255) attattATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGAAATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTaca > 1:53838/1‑140 (MQ=255) aGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaaa < 1:153843/140‑1 (MQ=255) aaaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAtt < 1:112568/140‑1 (MQ=255) aaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTCAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGCCGTACACCAAGAAAATTTGCAGTc > 1:79075/1‑140 (MQ=255) gggAATTTAAACGTCGCGCACAAGTCGGTAAACCTGGTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCAAGAAAAATAATAAAAAATACAATACGAACACCAAGAAAATTTGCTGTCATGCAATCAACt > 1:22402/1‑140 (MQ=255) ttAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGa > 1:82151/1‑140 (MQ=255) gcgcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAACATTTGATGTCATGCAATCAGCTGGAGGacatactagt > 1:239994/1‑134 (MQ=255) gcACAAGTCGGTAAACCTGTATCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACCTAATTCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATGTTATGGACa > 2:281248/1‑140 (MQ=255) cacaAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAt > 1:142767/1‑140 (MQ=255) aaGTCGGTAAACCTGTTTCTAATTGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc < 1:234551/140‑1 (MQ=255) aaGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc < 1:29196/140‑1 (MQ=255) aaCCTGTTTCTAATAGATGGGGAAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgttgtt < 1:199925/140‑1 (MQ=255) ccTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGATGTCAAGCAATCAACTGCAGGAGATTATGGACATGTCGCAGTGGTTGa > 2:244667/1‑140 (MQ=255) cTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGAATATTATGGACATGTCGCAGTAGTTAAACAAGta > 2:271216/1‑140 (MQ=255) ggggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAc < 1:273832/140‑1 (MQ=255) | CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAAC > USA300TCH1516_ALE/2679584‑2679846 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |