| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,231,470 | A→C | 45.3% | M39L (ATG→CTG) | stp → | Serine/threonine phosphatase stp |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,231,470 | 0 | A | C | 45.3% | 9.3 / 63.3 | 55 | M39L (ATG→CTG) | stp | Serine/threonine phosphatase stp |
| Reads supporting (aligned to +/- strand): ref base A (17/13); new base C (16/9); total (33/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.83e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC > USA300TCH1516_ALE/1231332‑1231608 | cAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATg > 2:538330/1‑141 (MQ=255) tAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACAACTTTTAGTTGTGAGTG‑ATGGTCTGGTTg > 2:419225/1‑141 (MQ=255) aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGcc > 2:213863/1‑141 (MQ=255) aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGcc < 2:257942/141‑1 (MQ=255) aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGTACTACATATGTATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCa < 2:208390/141‑1 (MQ=255) aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTAATGATACGGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACACCTTTTAGTTCTGTGTG‑ATGGTCTGGGTgtcaa > 2:251376/1‑137 (MQ=255) aCGAGGAAAAGAAAAATGCAAGAGGGACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCAt < 2:560114/141‑1 (MQ=255) aaaaACAAATGCTAGAGGCACAATTTTTTACTGAGACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTGTTTATAATCAACCTAATCAACGACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAg < 1:564085/141‑1 (MQ=255) aaGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACCACCTTTAATTACATTTA‑ATGGTATGGGTGGCCATAAAGCacg > 2:126067/1‑139 (MQ=255) aGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGga > 1:489215/1‑141 (MQ=255) aTGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑AGGGTATGGGTGGCCATAAAGCAGGAGAAGtt < 2:602739/141‑1 (MQ=255) tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGCAGTTGCaa > 1:11398/1‑141 (MQ=255) tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAAGCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCaa > 1:201616/1‑141 (MQ=255) tAGAGGCACAATTTTTTACGGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa > 1:335907/1‑141 (MQ=255) tAGAGGCACAATTTGTTACAGATACTGGACAACATAGAGATAAGCATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa > 1:335721/1‑141 (MQ=255) agGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTa < 2:381393/141‑1 (MQ=255) aTTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTgg > 1:508322/1‑140 (MQ=255) tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACa > 1:540952/1‑141 (MQ=255) tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTCTTGTGAGCATGG‑AGTGGCGGAAATAAACCAGGAGAAGTTGCAAGTAAATTTGTTACa > 1:138541/1‑141 (MQ=255) tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTGTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGCGAAGTTGCAAGTAAATTTGTTACa > 1:387365/1‑141 (MQ=255) ttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAg < 1:343061/141‑1 (MQ=255) aCTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGAt < 2:284696/141‑1 (MQ=255) cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCTAGTAAATTTCTTACAGATGAGTTGa < 1:307788/141‑1 (MQ=255) cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGa < 1:482276/141‑1 (MQ=255) aacaTAGAGGTAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTGGTTCTGTGTG‑ATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccg > 2:403740/1‑140 (MQ=255) aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc < 2:219975/141‑1 (MQ=255) aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc > 1:436638/1‑141 (MQ=255) caTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGt > 1:218369/1‑141 (MQ=255) aTAGAGATAAGAATGAGGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGtt > 1:304925/1‑141 (MQ=255) tAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGc < 1:213863/141‑1 (MQ=255) aGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCgg > 2:50281/1‑141 (MQ=255) aGAATGAAGATGCGGGTGGTAGTTTTTATAATCAAACTAATCAACAACTTTTAGTTATGTGTG‑ATGGTCTGGGTCGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGCAGCgg < 1:450231/141‑1 (MQ=255) aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGGGTTGAAATCCCGTTTTGACGCGGaaa > 1:260771/1‑141 (MQ=255) aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGaaa > 1:504331/1‑141 (MQ=255) gAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCACCAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAt < 2:64568/141‑1 (MQ=255) gATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCtt > 1:479998/1‑141 (MQ=255) gATGCGGGTGATATTTTTTATAATCATACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTAGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAATTTTGTTACAGATGAGTTGAAGTCCGGTTTTGAAACGGAAAATcat > 2:374415/1‑139 (MQ=255) aTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTta < 2:99368/141‑1 (MQ=255) gCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTtata > 2:244276/1‑141 (MQ=255) gggTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGGTGAGTTGAAATCCCGTGTTGAAGCGGAAAATCTTATAGa > 2:420483/1‑141 (MQ=255) ggtATTTTTTGTAATCCACCTAATCAACACCTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaa < 2:201616/141‑1 (MQ=255) gtATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaac > 1:154749/1‑141 (MQ=255) tttttATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCa < 1:280796/141‑1 (MQ=255) ttATAATCAAACTAATCAACAACTTTTAGTTATGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGc > 2:325933/1‑141 (MQ=255) taATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa > 1:89913/1‑141 (MQ=255) taATCAAACTAATCAAAAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa < 2:129013/141‑1 (MQ=255) cAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAAt > 1:258064/1‑141 (MQ=255) tAATCAACAACTTTTAGTTTCGTGTG‑ATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAACTGGtt < 2:342559/141‑1 (MQ=255) caacTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaat < 1:50281/141‑1 (MQ=255) acTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaataa < 1:217259/141‑1 (MQ=255) cTTTTAGATCTGTGTG‑ATGGCCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTaataat > 1:385094/1‑141 (MQ=255) tttAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAatat > 1:540520/1‑141 (MQ=255) gtgtg‑ATGGTATGGGTGGCCATAAAGCAGGAGATGTTGCAAGTAAATTTGATACAGATGAGTTGAACTCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAatatat < 1:416106/141‑1 (MQ=255) g‑ATGGTCTGGGTGGCCATAAAGAAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAAt > 2:492974/1‑141 (MQ=255) gTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATAAAAATTTTc > 2:104620/1‑141 (MQ=255) | CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC > USA300TCH1516_ALE/1231332‑1231608 |
| 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: ‑ |