| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 3,809,746 | C→A | 5.3% | pseudogene (164/669 nt) | rph ← | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 3,809,746 | 0 | C | A | 5.3% | 3675.3 / 115.5 | 1027 | pseudogene (164/669 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| Reads supporting (aligned to +/- strand): ref base C (467/502); new base A (26/31); total (494/533) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 7.85e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 1210 total aligned reads displayed.
TTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCC > CP009273/3809679‑3809813 | aCGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAgccctggc > 1:21621778/1‑65 (MQ=255) gAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAgccctggacctg > 1:6630956/1‑67 (MQ=255) aGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGa > 1:14030865/1‑67 (MQ=255) aGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGa > 1:37836418/1‑67 (MQ=255) cGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCt > 1:47435319/1‑68 (MQ=255) gTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGAcc < 1:12720567/66‑1 (MQ=255) tACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCttt < 1:45499846/67‑1 (MQ=255) tACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCttt < 1:25124187/67‑1 (MQ=255) gggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAgg > 1:36763024/1‑68 (MQ=255) ggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa > 1:22524984/1‑68 (MQ=255) ggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa > 1:16920295/1‑68 (MQ=255) ggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa > 1:5813122/1‑68 (MQ=255) ggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa > 1:37157169/1‑68 (MQ=255) ggTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa > 1:4333759/1‑68 (MQ=255) gtgtGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:39336357/1‑68 (MQ=255) gtgtGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGa < 1:26446258/67‑1 (MQ=255) tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:27007572/1‑67 (MQ=255) tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:11829263/1‑67 (MQ=255) tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:18600539/1‑67 (MQ=255) tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:48443866/1‑67 (MQ=255) tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGaa > 1:39668744/1‑67 (MQ=255) gTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGcgcg > 1:49624409/1‑67 (MQ=255) gTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGcgcg > 1:28198863/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:45135778/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:27701650/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:38754557/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:22017440/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:15688818/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:802083/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:36413974/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACg > 1:8409489/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:10849632/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:32710999/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:35232875/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:25561569/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:24020830/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:121114/68‑1 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGACCTGACCTTTCAGGAAGCGCGGCACg > 1:28670736/1‑67 (MQ=255) aCGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGACCTGACCTTTCAGGAAGCGCGGCACGc < 1:2314918/68‑1 (MQ=255) ggCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCctt < 1:19521270/67‑1 (MQ=255) ggCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCctt < 1:14394670/67‑1 (MQ=255) ggCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCctt < 1:3825361/67‑1 (MQ=255) ggCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCctt < 1:29280591/67‑1 (MQ=255) gcagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct > 1:48853439/1‑68 (MQ=255) gcagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct > 1:32101529/1‑68 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:4165651/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:4388664/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:50430200/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:5078253/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:7633566/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:46466266/67‑1 (MQ=255) cagcaTGCCGTACTCTGCGGGGATCCAGCCCTGGCCCTGCCCTTTAAGGAAGCCCGGCACGCcttct < 1:27430150/67‑1 (MQ=255) aagCCGTACTCTGCGGTGATCCAGCCCTGGCTCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCa < 1:47972799/64‑1 (MQ=255) aTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAAt > 1:9575682/1‑68 (MQ=255) aTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAAt > 1:29724443/1‑68 (MQ=255) tGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGc < 1:16615359/57‑1 (MQ=255) tGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCcttct < 1:20041714/62‑1 (MQ=255) tGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATa < 1:7217976/68‑1 (MQ=255) tGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATa < 1:17608545/68‑1 (MQ=255) tGCCGTACTCTGCGGTGATCCAGCCCTGGACCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATa < 1:34725252/68‑1 (MQ=255) gCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATag > 1:41351444/1‑68 (MQ=255) cGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTGAATagag < 1:17353517/68‑1 (MQ=255) aCTCTGCGGTGATCCCGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:19033250/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGc < 1:14972341/67‑1 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGc < 1:11136525/67‑1 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg < 1:5272729/68‑1 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:33823249/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:42529653/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:42923503/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:33173484/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:14654920/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:23591443/1‑68 (MQ=255) aCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCg > 1:46862110/1‑68 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt < 1:4089326/68‑1 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt < 1:34388691/68‑1 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt > 1:34140205/1‑68 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt < 1:49965540/68‑1 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt < 1:18158753/68‑1 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt < 1:21102570/68‑1 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt > 1:24644201/1‑68 (MQ=255) tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt > 1:40467643/1‑68 (MQ=255) tctGCGGTGATCCAGCCCTGGACCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGt > 1:51010841/1‑68 (MQ=255) tGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTac < 1:20560507/68‑1 (MQ=255) tGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTac < 1:31178552/68‑1 (MQ=255) tGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTac < 1:10125600/68‑1 (MQ=255) tGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTac < 1:26713487/68‑1 (MQ=255) ggTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTAcaca > 1:31542393/1‑68 (MQ=255) ggTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTAcaca > 1:8745558/1‑68 (MQ=255) gTGATCCAGCCCTGGCCCTGACCTTTCATGAAGCGCGGCACGCCTTCATCAATAGCGGCGGTAcaca > 1:42147783/1‑67 (MQ=255) gTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTAcaca > 1:39996407/1‑67 (MQ=255) gATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCAGGCCTTCTTCATTAGAGGCGGTACacaac < 1:9217264/67‑1 (MQ=255) gATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACacaac > 1:13455340/1‑67 (MQ=255) tCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACt < 1:35901068/68‑1 (MQ=255) ccctggccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGt > 1:15171598/1‑68 (MQ=255) ccctggccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGt > 1:30394063/1‑68 (MQ=255) cctggccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTa > 1:26156147/1‑68 (MQ=255) ccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc > 1:49347/1‑68 (MQ=255) ccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc > 1:4606023/1‑68 (MQ=255) ccctgACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc > 1:30844016/1‑68 (MQ=255) ccctgACCTTTCAGGAAGCGCGGAACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc > 1:44366721/1‑68 (MQ=255) | TTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCC > CP009273/3809679‑3809813 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |