| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 39,246 | C→T | 50.0% | A630T (GCT→ACT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 39,246 | 0 | C | T | 50.0% | ‑5.7 / 20.7 | 18 | A630T (GCT→ACT) | pbp | Beta‑lactam‑inducible penicillin‑binding protein |
| Reads supporting (aligned to +/- strand): ref base C (2/7); new base T (5/4); total (7/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.35e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 | |||||||||||
GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTA > USA300TCH1516_ALE/39109‑39385 | gATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTATTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCcat > 1:221019/1‑141 (MQ=255) cGTAGTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGata < 2:264900/141‑1 (MQ=255) cggTTCTCAGATATCTTATCATACACTTTACCTGAGATCTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTACTAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAAtt < 2:16905/139‑1 (MQ=255) tcATATAGCTCATCCTACCCTTTACCTGAGATTTTGGCTTCGCAGGCTTCTTGTTCTTT‑ATCGTGTACATCATTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTg < 1:161777/141‑1 (MQ=255) tcatACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGACTATCTTTATCGTATGATATAAACCACCCAATTTGTCGACCAGTTtctcat > 2:236429/1‑139 (MQ=255) ctACACTTTTCCTGAGATTTTGGCATTGTAGCTAGCCATAACTTTAATCCACAACCT‑TTAATGACTAATAGTCATCATTATGTTTCTAGTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTg < 2:332277/140‑1 (MQ=255) acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt < 1:189813/141‑1 (MQ=255) acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt < 1:255979/141‑1 (MQ=255) gagaTTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGt > 2:117440/1‑141 (MQ=255) gcCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGAGTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCa > 1:229218/1‑141 (MQ=255) cATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt < 1:117440/141‑1 (MQ=255) cATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt < 2:26007/141‑1 (MQ=255) ttCTTTT‑ACCTTGTACATCTTCAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTa < 1:91423/141‑1 (MQ=255) tCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCa > 2:293478/1‑141 (MQ=255) tCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCa < 2:339303/141‑1 (MQ=255) aaTAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAtcttc > 2:283892/1‑141 (MQ=255) aTAGCGATCATCATGTTTGGATTATCCTTATCATATGATATAAACCTCCCCATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCACTAACGGATTTTCCAATTAAGTTTGCATAAGATCTATAAATAtattct < 2:226490/141‑1 (MQ=255) gCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa > 1:104871/1‑141 (MQ=255) | GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTA > USA300TCH1516_ALE/39109‑39385 |
| 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: ‑ |