| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,502,887 | (A)5→6 | coding (1411/2106 nt) | melR_2 → | Melibiose operon regulatory protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,502,882 | 1 | . | A | 96.9% | 109.8 / ‑2.6 | 32 | coding (1406/2106 nt) | melR_2 | Melibiose operon regulatory protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (12/19); total (12/20) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01 | |||||||||||
TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT > USA300TCH1516_ALE/2502736‑2503010 | tCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTTAAAATTC‑a > 3:84941/1‑148 (MQ=255) aaaattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaa‑aact < 4:17612/148‑4 (MQ=255) aattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaa‑aactgc > 4:188087/1‑143 (MQ=255) aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACAt < 3:244594/148‑1 (MQ=255) aaaaaTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCtt < 3:368288/148‑1 (MQ=255) aTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACAt > 1:45012/1‑141 (MQ=255) aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAAc < 3:273836/148‑1 (MQ=255) aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTAATCAAACATAAAACAAGTTTATAATGTCATGCAGCGTCTAAAATTCCATTACTACTTTATTTATAAAAAAAAATAAAAAA‑ACTGCAACACAACTTAACACTAAAAAc < 4:240870/148‑1 (MQ=255) aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 3:249376/1‑148 (MQ=255) aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 3:238454/1‑148 (MQ=255) aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAac > 4:309489/1‑148 (MQ=255) aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAAc > 3:386394/1‑148 (MQ=255) cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa < 4:263328/148‑1 (MQ=255) cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa < 3:49801/148‑1 (MQ=255) aTGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGaca < 3:46049/148‑1 (MQ=255) ggCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt > 3:248183/1‑148 (MQ=255) tttttAGAAACTTATTCAAACGTGAAACAAGTTTATAATGACATTCAGCATCTTAAATTCCATTATTACTTTATTAATAAAAAAAAATCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAt < 4:286858/148‑1 (MQ=255) ttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtttt < 4:301221/148‑1 (MQ=255) ttACAAACTTATTCAACCGAGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAACACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGacac < 2:50730/141‑1 (MQ=255) aaCTTATTCACCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa < 3:355651/148‑1 (MQ=255) aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa < 3:355653/148‑1 (MQ=255) cAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGa < 4:248183/148‑1 (MQ=255) aaCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa < 3:380535/148‑1 (MQ=255) tGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAattta < 4:347847/148‑1 (MQ=255) ggAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAatttat < 3:149173/148‑1 (MQ=255) aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTAtttt > 4:195533/1‑148 (MQ=255) cAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTa < 4:125307/148‑1 (MQ=255) tttATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGAtt > 3:51289/1‑148 (MQ=255) gTCATGCAGCGTCTTAAATTCCATTAGTACTTTATTGATAAAAAAAAAACAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtata < 4:45503/148‑1 (MQ=255) tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt < 4:109694/148‑1 (MQ=255) tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt < 4:46386/148‑1 (MQ=255) ccATTATTACTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGtata > 4:1077/1‑148 (MQ=255) tattaCTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 4:361432/1‑148 (MQ=255) tactaCTTTATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat > 4:98863/4‑148 (MQ=255) ttATTGATATTGAAAATTCAAAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACctgt > 3:148889/1‑148 (MQ=255) | TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAA‑ACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT > USA300TCH1516_ALE/2502736‑2503010 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |