| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP006881 | 53,413 | G→A | 100% | intergenic (+45/‑94) | U712_00230 → / → U712_00235 | Protein sspF/4‑diphosphocytidyl‑2‑C‑methyl‑D‑erythritol kinase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006881 | 53,413 | 0 | G | A | 98.4% | 195.2 / ‑4.0 | 62 | intergenic (+45/‑94) | U712_00230/U712_00235 | Protein sspF/4‑diphosphocytidyl‑2‑C‑methyl‑D‑erythritol kinase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (27/34); total (28/34) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.52e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.99e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
GTGAAATTCGGGCCCGCGATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTGGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGAAAAAGCGCCAGC > CP006881/53277‑53541 | gTGAAATTCGGGCCCGCGATGCAGGTAACATGGTGAAGCGTTCTTTTGAAATCGCCGAAGAGCAAATGGCTCAGAATCAGAATTACCGATAAGGATGTGACCCGGGGGACGTGATGTTCCCTGTTTTTTTTATTTTAGa < 8:238432/139‑1 (MQ=255) tGAAATCCGGGCCCGGGATGCCGGTAACATGGGTAAGCGTGCTATTTAAATCGCCGAACTGAAAATGCCTAATATTACTAATAACCGATACGGATGTTACCC‑GGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGata < 6:106600/139‑1 (MQ=255) aaaTTCGGGCCCGCGATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGatat < 8:192048/139‑1 (MQ=255) tttggggCCCGCGATGCCGGTAACATGGTGAATCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCGCTGGTTTTTTTATTTTAGATATaa < 6:48531/135‑1 (MQ=255) aTTCGGGCCCGCGATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATaa < 6:257184/139‑1 (MQ=255) cgATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATgg > 6:277077/1‑139 (MQ=255) gATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATggg < 1:67001/139‑1 (MQ=255) gATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATggg < 5:137526/139‑1 (MQ=255) ccGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTg > 6:76279/1‑138 (MQ=255) gTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAata < 6:247239/139‑1 (MQ=255) cATGGTGAAGCGAGCTATTGAAAGCGCCGGACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTATAGATATAAATACATAATGGGCTGAATATGGa < 6:172859/139‑1 (MQ=255) cATGGTGAAGAGCGCTATTGAAATCGCCGTACAGCAAATGGCTCAGAATCAGAATAACCGCTAAGGATGAGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGTGCTGAATATGGa < 6:81621/139‑1 (MQ=255) ggTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGatat > 7:85364/1‑139 (MQ=255) ggTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGatat > 7:260640/1‑139 (MQ=255) ggTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAAGGTGCTGAATATGGatat > 6:173184/1‑139 (MQ=255) aaGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGtt > 3:19724/1‑138 (MQ=255) gCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGt > 4:148858/1‑135 (MQ=255) gCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGt < 3:148858/135‑1 (MQ=255) cGTGCTATTGAAATATCCGAACAGCAAATGGCTCAGAATCAGAAAAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGCTTTTTTTATTTAAGATATAAATACATAATGGGATGAATATGGATATGtctgtc > 7:168587/1‑134 (MQ=255) gTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATcc > 5:53018/1‑139 (MQ=255) tGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCt > 1:83139/1‑139 (MQ=255) cTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAAGCGATATTGATGTGACCCTGGGGACGTGCTGTTGCCTGGTTTTTTTATTTTAGATATAATTACATAATTGGCTGAATATGGATATGTTCATCCTg < 3:181831/138‑1 (MQ=255) cTATTGAAATCGCCGAACAGCAAATGGCGCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTg < 2:32299/138‑1 (MQ=255) tCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAAt < 5:97090/139‑1 (MQ=255) gCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAAtgt > 1:182052/1‑139 (MQ=255) gCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAAtg < 2:83139/138‑1 (MQ=255) cAGCAAATTGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACa < 8:284327/139‑1 (MQ=255) cAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACa < 5:277077/139‑1 (MQ=255) aGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACaa < 8:85364/139‑1 (MQ=255) aaaagtcTCAGAATCAGAATAACCTATAATGATGTGACCCGGGTGACGGGCTGTTCCCTGGTTATTTTATTTTAGATATAAATACATACTGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGt < 6:170019/133‑1 (MQ=255) aaTGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGtt < 8:216276/139‑1 (MQ=255) tGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCa < 4:19724/139‑1 (MQ=255) tcagaatcagaaTAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGata > 7:54662/1‑99 (MQ=255) tcagaatcagaaTAACCGATAAGGATGTGACCAGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGata < 8:54662/99‑1 (MQ=255) agaatcagaatAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTg < 3:218980/108‑1 (MQ=255) agaatcagaatAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTg < 3:273605/108‑1 (MQ=255) agaatcagaatAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTg > 4:218980/1‑108 (MQ=255) agaatcagaatAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTg > 4:273605/1‑108 (MQ=255) agaatAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGttt < 6:53018/138‑1 (MQ=255) aCCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGTATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATg > 5:281451/1‑137 (MQ=255) aCCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGat > 8:25408/1‑84 (MQ=255) aCCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGat < 7:25408/84‑1 (MQ=255) aCCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATgg < 2:182052/138‑1 (MQ=255) aCCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATg > 5:104846/1‑137 (MQ=255) aaGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCaa > 5:194215/1‑98 (MQ=255) aaGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCaa < 6:194215/98‑1 (MQ=255) tgtgACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTg > 7:141820/1‑138 (MQ=255) gtgACCCGGGGGACGTGCTGTTCCCTTGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGa < 5:173184/138‑1 (MQ=255) tgACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGa > 1:117948/1‑137 (MQ=255) tgACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGAGGGAGAAGTAGGTGa > 5:174590/1‑137 (MQ=255) gagccGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATTGGCTGAATAGGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAg < 4:103424/136‑1 (MQ=255) aCCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATACTGTACTTCAAATGAGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGc > 7:170389/1‑139 (MQ=255) gggggACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCt > 3:126952/1‑55 (MQ=255) gggggACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCt < 4:126952/55‑1 (MQ=255) ggggACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGc > 5:57332/1‑139 (MQ=255) ggggACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGc > 7:85268/1‑139 (MQ=255) ggggACGTGCTGTTCCCTGGTTTTTTTATTTTAGATATAAATAAATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTGGGTGAAAGCTATGc > 7:172794/1‑139 (MQ=255) cGTGCTGTTCCCTGGTTTTTTTATTTTGGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTAtt > 5:40578/1‑139 (MQ=255) ttCCCTGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGaa > 1:4724/1‑138 (MQ=255) tgttttttttATTTTATATAAAAAAACATACTGGGCTGAATATTGATATGTTAATCCTGAAATAAAAATGTCATCCAATGTTAATACTTCTGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGAAAAcgcg < 6:93059/136‑1 (MQ=255) tGGTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGAAAAcgcg < 8:85268/139‑1 (MQ=255) gTTTTTTTATTTTAGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGAAAAAgcgc < 8:141820/138‑1 (MQ=255) ttttattttaGATATAAATACATAATGGGCTGAATATGGATATGTTCATGCTTTACTTCAAATGTTATACAATGTTCATACTTATGTTTATATGGAGAAGTAGGTGAAAGCTATGCCTATTTTATAAAAAGCGCCAGc < 2:53060/138‑1 (MQ=255) | GTGAAATTCGGGCCCGCGATGCCGGTAACATGGTGAAGCGTGCTATTGAAATCGCCGAACAGCAAATGGCTCAGAATCAGAATAACCGATAAGGATGTGACCCGGGGGACGTGCTGTTCCCTGGTTTTTTTATTTTGGATATAAATACATAATGGGCTGAATATGGATATGTTCATCCTGTACTTCAAATGTGATACAATGTTCATACTTATGTTTAGATGGAGAAGTAGGTGAAAGCTATGCGTATTTTAGAAAAAGCGCCAGC > CP006881/53277‑53541 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |