| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 1,461,169 | C→T | 5.9% | pseudogene (1521/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 1,461,169 | 0 | C | T | 5.9% | 1126.1 / 30.9 | 359 | pseudogene (1521/2513 nt) | ydbA | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| Reads supporting (aligned to +/- strand): ref base C (146/183); new base T (15/6); total (170/189) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.23e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Only 100 of 475 total aligned reads displayed.
TCGGTATCCAGATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATG > CP009273/1461102‑1461236 | tCGGTATCCAGATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATggc > 1:25373869/1‑68 (MQ=255) ggTATCCAGATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATggcg > 1:22038775/1‑67 (MQ=255) agTATCCAGATCGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATggcg > 1:14791636/2‑67 (MQ=255) tATCCAGATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATggcggc > 1:23777055/1‑67 (MQ=255) tCCAGATAGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcacc < 1:27631856/68‑1 (MQ=255) gATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggccccggc > 1:21131770/1‑67 (MQ=255) gATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc > 1:18945633/1‑67 (MQ=255) gATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc > 1:11755310/1‑67 (MQ=255) gATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc > 1:24012206/1‑67 (MQ=255) gATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGACCACTATCACCAATGGcggcaccggc > 1:23254926/1‑67 (MQ=255) ttGACGGCGACCAGGCGATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc < 1:17975831/65‑1 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggcac > 1:18286733/1‑67 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggcac > 1:3185651/1‑67 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggcac > 1:3902161/1‑67 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggcac > 1:10984096/1‑67 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggcac < 1:5491286/67‑1 (MQ=255) ttGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc < 1:10361396/65‑1 (MQ=255) ttGACGGCGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGcggcaccggc < 1:6462677/65‑1 (MQ=255) atGACGGGGACCTTGCCATCGTATATAAGGAAGCCTTGATCTCTATCACCAATGGcggcaccggc < 1:15467972/64‑1 (MQ=255) gACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCa < 1:19338952/68‑1 (MQ=255) gACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCa < 1:20525435/68‑1 (MQ=255) gACGGCGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCa < 1:25622245/68‑1 (MQ=255) cGGCGACCAGGCGTTTGTAAAAAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGa < 1:23600376/68‑1 (MQ=14) cGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGa < 1:24669121/68‑1 (MQ=255) ggCGACCAGGCCATCGTCAATAACGATGGCGAGAGCACTATCACCAATGGCGGCACCGGAACTCAGa > 1:26022309/1‑67 (MQ=255) ggCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGa > 1:26526515/1‑67 (MQ=255) gACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCa < 1:22263271/67‑1 (MQ=255) gACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCa < 1:12583328/67‑1 (MQ=255) gACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCa < 1:17123833/67‑1 (MQ=255) aCCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAAc < 1:23122203/68‑1 (MQ=255) ccAGGCGTTTGTTAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACg < 1:25793526/68‑1 (MQ=17) gCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGAGGCACCGGCACTCAGATCAAAGGTa > 1:2928046/1‑67 (MQ=11) cgttCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGt < 1:15128628/62‑1 (MQ=255) ccATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAac > 1:7430515/1‑68 (MQ=255) ccATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAac > 1:18517749/1‑68 (MQ=255) ccATCGTCAATAACGAAGGCGAGAGCACAATCACCAATGGAGGCACCGGCACTCAGATCAACGGTAac > 1:16288476/1‑68 (MQ=18) cATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacg < 1:7800048/68‑1 (MQ=255) tCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacgac < 1:7951225/68‑1 (MQ=255) tCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacgac < 1:20917548/68‑1 (MQ=255) gTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacgacg > 1:1725708/1‑67 (MQ=255) gTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacgacg > 1:13427546/1‑67 (MQ=255) gTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAacgacg > 1:10022769/1‑67 (MQ=255) tCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGc > 1:4413634/1‑67 (MQ=255) aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCAcc > 1:24472865/1‑68 (MQ=255) aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCAcc > 1:8800297/1‑68 (MQ=255) aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCAcc > 1:2909652/1‑68 (MQ=255) aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCAcc < 1:22432595/68‑1 (MQ=255) aaCGAATGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:24242925/68‑1 (MQ=255) aaCGAAGGCGAGAGCTCTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:12791312/68‑1 (MQ=255) aaCGAAGGCGAGAGCTCCATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:12193682/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:1314269/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:11308086/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:18725732/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:26912729/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:27317193/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:27885911/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:16878869/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:10581354/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:20731672/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:4857565/68‑1 (MQ=255) aaCGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACcgc < 1:4133263/68‑1 (MQ=255) cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGa > 1:28407421/1‑68 (MQ=255) cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGa < 1:28701199/68‑1 (MQ=255) cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGa > 1:12969015/1‑68 (MQ=255) cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGa > 1:9815908/1‑68 (MQ=255) aaGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACTCAGATAAACGGTAACGACGCCACCGCGAAt > 1:17619822/1‑68 (MQ=11) aGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATa > 1:25924872/1‑68 (MQ=255) ggCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATa > 1:2256018/1‑67 (MQ=255) ggCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATa > 1:28076943/1‑67 (MQ=255) cGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAAc < 1:22781760/67‑1 (MQ=255) cGAGAGCACCATCACCAACGGTGGCACCGGCACGCAGATCAACGGTAACGACGCCACCGCGAATAACa > 1:14907723/1‑68 (MQ=14) cGAGAGCACCATCACCAACGGTGGCACCGGCACACAGATAAACGGTAAAGACGCCACCGCGAAAAACa > 1:16179894/1‑68 (MQ=11) gagaGCACTATCACCAATGGCTGCACCGGAACTCAGATCAACGGTAACGACGACACCGCGAATAACAg > 1:28598939/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTg < 1:20253836/66‑1 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:13982877/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:697395/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:5835413/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:20010038/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:9378950/1‑68 (MQ=255) gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGa > 1:25044351/1‑68 (MQ=255) tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGaaaaa < 1:2519077/68‑1 (MQ=255) tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGaaaaa < 1:15897480/68‑1 (MQ=255) tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGaaaaa < 1:2620157/68‑1 (MQ=255) caTCACCAACGGTGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTgg < 1:17518460/62‑1 (MQ=18) aTCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGaaaaa > 1:21432508/1‑67 (MQ=255) aTCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAc < 1:15620363/68‑1 (MQ=255) cACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:3717706/1‑67 (MQ=255) aCCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:10727132/1‑66 (MQ=255) cAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:7550195/1‑64 (MQ=255) cAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:24852815/1‑64 (MQ=255) cAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:2178098/1‑64 (MQ=255) cAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAcc > 1:27080346/1‑64 (MQ=255) cAACGGTGGCACCGGCACGCAGATGAAGGGTGACGACGCCACCGCGAATAACAGTGGAAAAACCAcgg > 1:13890544/1‑66 (MQ=14) aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGt < 1:5215811/68‑1 (MQ=255) aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGt < 1:4626551/68‑1 (MQ=255) aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGt < 1:14435440/68‑1 (MQ=255) aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGtt > 1:16498941/1‑68 (MQ=255) ggcggcACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGa > 1:19713795/1‑68 (MQ=255) ggcggcACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGa > 1:8265135/1‑68 (MQ=255) cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATg > 1:678915/1‑68 (MQ=255) | TCGGTATCCAGATTGACGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATG > CP009273/1461102‑1461236 |
| 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: ‑ |