| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,289,113 | T→C | 14.4% | Q126R (CAA→CGA) | cdaA ← | Cyclic di‑AMP synthase CdaA |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,289,113 | 0 | T | C | 14.4% | 54.6 / 5.4 | 28 | Q126R (CAA→CGA) | cdaA | Cyclic di‑AMP synthase CdaA |
| Reads supporting (aligned to +/- strand): ref base T (10/14); new base C (2/2); total (12/16) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-02 | |||||||||||
TAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATT > USA300TCH1516_ALE/2288979‑2289247 | tAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTATCCATATATTGCACAg > 1:42318/1‑141 (MQ=255) gTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCt > 1:191953/1‑141 (MQ=255) aGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGaaa < 2:116066/141‑1 (MQ=255) cagtaattaaAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCg < 2:221376/138‑1 (MQ=255) attaattaAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGa < 2:115839/141‑1 (MQ=255) ttaaAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGaa < 2:191953/141‑1 (MQ=255) aaaaCTTCTTGCGAAACATTTGAATCAATTGCAATACCTGTTTCAAGATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATc < 1:4860/141‑1 (MQ=255) aaGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCaa < 1:146189/141‑1 (MQ=255) aaGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCaa > 1:210329/1‑141 (MQ=255) cTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTtct > 1:281824/1‑141 (MQ=255) gCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTCATGCACCTATACGTCTTGTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCtt < 2:147775/141‑1 (MQ=255) gCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATCGAATCAATTTCTCtt < 1:266453/141‑1 (MQ=255) ccATTGCAATACCTGTTTCAATATCATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACg < 1:296098/141‑1 (MQ=255) ccATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACg < 2:85111/141‑1 (MQ=255) aaTACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTTTTCATCTTTTTTATACGTATTata > 2:160015/1‑139 (MQ=255) tCAATATAATCTTGAAGACCTGTTTCTTTTTCAAGGACAATTAATGCACCTATACGTCTTTTAGCCATATATCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGt > 2:163942/1‑141 (MQ=255) tCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGt > 2:330352/1‑141 (MQ=255) cAATATAATCTTGAAGACCTGTTTCTTTTTGAAAGACAATTAATGCAGCTATACGTCTTTTAGCCATATATTGCACAGCCTTTTAAACCGTTTGACTCAATTTCTCTTCATATTTACTATACGTATTAGAAGTATAGGGtt > 1:102133/1‑141 (MQ=255) ataATCCTGAAGACTTTCTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGAGTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTaa < 1:207327/141‑1 (MQ=255) gAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTAc > 1:358715/1‑141 (MQ=255) aaGATCTGGTTCTTTTTCAAAGACAATTTATGCCCCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTTTACGTATTAGAAGTATAGCGTTTTAAAAAGCTAcc < 2:138597/141‑1 (MQ=255) tGTTTCTTTTTCAAAGACAATTAATGCACCTATGCGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTTTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTAcc < 2:20705/141‑1 (MQ=255) aCAATTACTGCACCTTTACGTATTTTAGTCATATATTGCACCGCCTTTGAAGCCGATTACATAAATGTCGCTTCCACTTTACTAGACGCATTTGCAGTAGAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCGAACGCa > 2:131780/1‑141 (MQ=255) aCAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCa > 2:253590/1‑141 (MQ=255) aCGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTg < 1:164900/141‑1 (MQ=255) tAGCCATATATTGCACAGCCTTTGCCACCAATGGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTa > 1:85238/1‑141 (MQ=255) atatatCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTAtt < 1:330352/141‑1 (MQ=255) atatatCGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTAtt < 1:163942/141‑1 (MQ=255) | TAGGTATAAAGACATTAATTAAAAGTTCTTGCGAAATATTTGAATCCATTGCAATACCTGTTTCAATATAATCTTGAAGACCTGTTTCTTTTTCAAAGACAATTAATGCACCTATACGTCTTTTAGCCATATATTGCACAGCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATT > USA300TCH1516_ALE/2288979‑2289247 |
| 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: ‑ |