| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 19,009 | C→T | 24.2% | S222F (TCC→TTC) | gdpP → | Cyclic‑di‑AMP phosphodiesterase GdpP |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 19,009 | 0 | C | T | 24.2% | 37.7 / 10.8 | 25 | S222F (TCC→TTC) | gdpP | Cyclic‑di‑AMP phosphodiesterase GdpP |
| Reads supporting (aligned to +/- strand): ref base C (3/16); new base T (3/3); total (6/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.25e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01 | |||||||||||
TTATTTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGAA > USA300TCH1516_ALE/18876‑19145 | ttattTTTAGATCCCTACGGGGAGATTACGGAAAATATGCATGATACGCAGCGTTCGGACATCAACTCAGTGGTAACGCGTGTCATTAGTCGTTGGGCATCAGCGTATAATATTTTTTTCAAAAGATACAGTTCCGATCaa < 2:245164/141‑1 (MQ=255) tttAGATAACTACGATGAGATTACGCAAAATATGAGTGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGt > 1:307337/1‑141 (MQ=255) gATAATTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGcc < 1:149898/141‑1 (MQ=255) gATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGTTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGcc < 1:251706/141‑1 (MQ=255) gATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGGTCGGAAATCAACTCAAAGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGCTCAATTCGTAGcc > 1:13431/1‑141 (MQ=255) aaTAACTACGATGAGATTAACCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGcc < 1:149892/140‑1 (MQ=255) gagaTTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCaa < 1:131639/141‑1 (MQ=255) cGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAatat < 1:122815/141‑1 (MQ=255) aaTATCAAAGATAAGGAGCGATCGGAAATCAACTCAATGGTAACGCGTTTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCt < 2:163736/141‑1 (MQ=255) gTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAAt < 1:129811/141‑1 (MQ=255) cGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTg < 2:17195/141‑1 (MQ=255) aTCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATc < 1:240274/141‑1 (MQ=255) cAACTCAAGGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTCGCCTATTTAACTAAAGAAATATTAGCTGACTTAGAAGAATCCAAATTTGaaacatt > 2:358243/1‑135 (MQ=255) taaGTCGATGGGCAACTGAGTATAAAATATTTTTCAAAAGATACATTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAgtg < 2:159461/139‑1 (MQ=255) gTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTg < 1:285448/141‑1 (MQ=255) gTCGATGGGAAAATGTGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTg < 1:327629/141‑1 (MQ=255) tGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTAt > 2:349701/1‑141 (MQ=255) gggCAACTGAGAATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATc < 2:295912/141‑1 (MQ=255) ataataTATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTaa < 2:273748/141‑1 (MQ=255) atatatTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACAt < 1:284673/141‑1 (MQ=255) tttttCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGt > 1:131233/1‑141 (MQ=255) cAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCgg > 1:123193/1‑141 (MQ=255) acaacgTTCCGAACAATACGTAGACTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTCGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTgg < 1:118204/136‑1 (MQ=255) aCAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAAAAGTACACGCCGTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTg < 1:86317/141‑1 (MQ=255) aGTGCCGATAAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGaa < 2:13431/141‑1 (MQ=255) | TTATTTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGAA > USA300TCH1516_ALE/18876‑19145 |
| 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: ‑ |