| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 382,916 | C→A | 23.0% | G331C (GGT→TGT) | ulaA ← | Ascorbate‑specific PTS system EIIC component |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 382,916 | 0 | C | A | 23.0% | 124.2 / 24.6 | 59 | G331C (GGT→TGT) | ulaA | Ascorbate‑specific PTS system EIIC component |
| Reads supporting (aligned to +/- strand): ref base C (19/26); new base A (9/5); total (28/31) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.21e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
ATTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACG > USA300TCH1516_ALE/382776‑383052 | aTTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATAcc > 2:511332/1‑141 (MQ=255) tAGAGCGGCGACAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGAt > 1:442314/1‑141 (MQ=255) agagCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATg > 1:327925/1‑141 (MQ=255) gagCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGa > 2:529949/1‑141 (MQ=255) gcgcCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCt < 2:64162/141‑1 (MQ=255) cgcCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATACGATAAACATACCGATGACACCTg < 2:283133/141‑1 (MQ=255) gcCAGCAATAGCACCTTTAATACCGCCTCTTTCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGt < 2:248366/141‑1 (MQ=255) gCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGtaata > 1:134106/1‑141 (MQ=255) cAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAACCATACCGATGACACCAGtaataa > 1:487806/1‑141 (MQ=255) aCCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGAc < 1:381002/141‑1 (MQ=255) tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa < 2:130340/141‑1 (MQ=255) tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa > 2:553582/1‑141 (MQ=255) tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa > 1:407147/1‑141 (MQ=255) tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa > 1:402019/1‑141 (MQ=255) tttAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCAACAAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACaaa > 2:553532/1‑141 (MQ=255) ttAATACCGCCTCTGGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAg > 1:424178/1‑141 (MQ=255) aCCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATcc > 2:104522/1‑141 (MQ=255) cGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACGAAGAATCCaa < 1:442326/141‑1 (MQ=255) ctTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTCCGCCCGGTAAAATGACGACGCCACCAAATAAGAATACCAAAAACATACAGATGCCACCTGTAATAAAGCAGAAAAAGAACCCAATTAAt > 1:275191/1‑141 (MQ=255) ttGCATTACCTAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATa < 2:241904/141‑1 (MQ=255) gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACt < 2:329746/141‑1 (MQ=255) gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGGAATAAAGCTGACAAAGAATCCAATTAATACt > 1:274444/1‑141 (MQ=255) gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACt < 1:22640/141‑1 (MQ=255) gCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAACAAGAATAAGATAAACATACAGAAGACACCGGTAAAAAAACTCACAAAGAATCCAATTAATAca > 2:446569/1‑140 (MQ=255) cATGACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACCACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTg < 1:189922/141‑1 (MQ=255) tACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCAt < 2:53621/141‑1 (MQ=255) aaTACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTtgt > 1:252604/1‑141 (MQ=255) aCAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGAAAAATGACGCCGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCCATTAATACTGCATTTTGTGCa > 2:100037/1‑141 (MQ=255) caggCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACGCCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCCTatg > 1:439072/1‑139 (MQ=255) cagcCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAg < 1:537377/141‑1 (MQ=255) cagcCGCTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAg < 1:537473/141‑1 (MQ=255) actggtccACCTAAGAAGAAGCGTGCAACTACGCCAGGTAAAATGCCGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATCCTGCATTTTGTGCATAAggg > 2:462449/8‑141 (MQ=255) tGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAacac > 2:605194/1‑141 (MQ=255) gCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATCAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAGcaca > 2:355222/1‑141 (MQ=255) ccTAAGAAGAAGGGTGCAACTACGGCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAGTAAAGCTGACAAAGAATCCCATTAATACTGCATTTTGTGCATAAGGGAACACAATa < 1:115110/141‑1 (MQ=255) aagaagaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAggg < 2:14818/141‑1 (MQ=255) aagaagaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAggg < 1:488121/141‑1 (MQ=255) agaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCACTTAATACTGCATTTTGTGCATAAGGGAACACAATAGAGCAGt > 2:390640/1‑141 (MQ=255) aaaagTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGt < 1:574685/139‑1 (MQ=255) agTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTa < 2:110512/141‑1 (MQ=255) agTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTa > 1:517478/1‑141 (MQ=255) gtgtGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTaa < 2:63438/141‑1 (MQ=255) gtgCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATg < 2:442851/141‑1 (MQ=255) gCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCa < 1:97398/141‑1 (MQ=255) cTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAAAAGGGCAGTCTAATGCAGGtt < 1:370274/141‑1 (MQ=255) tAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTgg > 1:486580/1‑141 (MQ=255) ctccaccaACTAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt < 1:195763/139‑1 (MQ=255) cgCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt < 1:22403/141‑1 (MQ=255) cgCCACCAAATAAGAATAAGATAAACATACAGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCtttt > 1:161338/1‑141 (MQ=255) caccaAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAg < 1:355222/141‑1 (MQ=255) aaaTAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAAt < 1:529949/141‑1 (MQ=255) taagaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGGACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTct > 1:43583/1‑140 (MQ=255) agaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCtt > 2:455311/1‑141 (MQ=255) gaataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCttt < 1:244702/141‑1 (MQ=255) gaataagaTAAACATACAGATGACACGAGTAATAAAGCTGACAAAGAATACAATTAATACTGCATTTTGTACATAAGAGAACACGATAGGGCCGACTAATACAGGATCAGAATTTGGTACAAGCTTTTCAGGAATTGCttt > 2:16168/1‑141 (MQ=255) aataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTa < 1:241939/141‑1 (MQ=255) aataagaTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTa < 1:605194/141‑1 (MQ=255) aTAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCt < 1:583916/141‑1 (MQ=255) aCATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGa > 2:494052/1‑141 (MQ=255) aTACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACg < 2:517478/141‑1 (MQ=255) | ATTTAGAGCGGCGCCAGCAATAGCACCTTTAATACCGCCTCTTGCATTACCGAATACAGCAGCCGTTGCACCTAAGAAGAAGTGTGCAACTACGCCAGGTAAAATGACGACGCCACCAAATAAGAATAAGATAAACATACCGATGACACCTGTAATAAAGCTGACAAAGAATCCAATTAATACTGCATTTTGTGCATAAGGGAACACAATAGGGCAGTCTAATGCAGGTTTAGAATTTGGTACAAGCTTTTCAGAAATTCCTTTAAATGCTGGGACG > USA300TCH1516_ALE/382776‑383052 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |