| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,222,233 | 0 | G | A | 42.9% | 75.9 / 21.3 | 56 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| Reads supporting (aligned to +/- strand): ref base G (28/4); new base A (0/24); total (28/28) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 9.40e-12 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTG > NC_000913/1222085‑1222382 | gtgAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTAGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGaa < 2:990290/151‑1 (MQ=255) aaaGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAat > 2:454102/1‑150 (MQ=255) gTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATaa < 2:100979/151‑1 (MQ=255) gATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATc > 1:630538/1‑151 (MQ=255) aTGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATc‑c < 2:171319/151‑1 (MQ=255) tGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATc‑cc > 2:411468/1‑151 (MQ=255) gAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGtt > 1:193123/1‑151 (MQ=255) aaTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCt > 2:101110/1‑151 (MQ=255) tGGGGGAAATTAAACTTGGCGTAAATGGTAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTaaa > 2:73882/1‑150 (MQ=255) gaaaaTTAAACGGGGCGAAAAGGGCACCCGGAACCCAGCGGCCAGCGTGTGGGGAAGGGGGGGGGGCAGGGGGGTGATAATGGCTACAATGACACCGCGGGGAGGGGGGGCGTAAAATATAAGTTCTGTCC‑CCGCCGTTAGCTAAAAAAcc < 1:19921/149‑1 (MQ=255) gAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACcg > 2:734412/1‑151 (MQ=255) aaaTTAATCTTGGCTTAAAGGGCACCTTAACCCCAGCGGCCAGCGTCGGGGAAATGTGGGGGTGCAGCTGGGTGATAATGGCTAAAAGCACCCCGCATTGATGGGGGGCCAAAATTATATGTTCTGCCC‑CCGCCGTTAGCTAAAAAACcgc < 2:194299/151‑1 (MQ=255) aaTAAATCTTGGCTAAAAGGGCACCTTAAACCCAGCGGCCAGCGTCGGGGGATTGGGGGGGTGCGGCGGGGTAATAAGGGCTAAAACGCCCCCGCAGTGGTGGTGGGCCTAAAATAAAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACcgcg < 2:907923/151‑1 (MQ=255) aaaCTTGGCGTAAATGGCACCCTGAACCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGTTGGGTGATAAGGGCTACAATGACCCCGCAGTGATGGTGGGCCTAAAATATAAGTTCTGACC‑CCGCCGTTAGCTAAAAAACCGcgtcg < 2:257546/150‑1 (MQ=255) ttGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTc > 1:834400/1‑151 (MQ=255) tGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTc > 1:659573/1‑150 (MQ=255) cGTAAAGGGCACCCTAAACCCAGCGGCCGGGGTGTGGGGATTGGGGGCGTGCGGCTGGGTGAAAATGGCTACAAGGCCACCGAAGTGATGGGGGGCCTAAAATATAATTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCa < 2:458995/148‑1 (MQ=255) aaaTGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcg > 2:679279/1‑151 (MQ=255) aaTGGCACCCTGAACCCAGCGGCCAGCGTCTGGGGAATGGGGGCGTGCAGCTGGGTGATAAGGGCTACAATGACCCCGCAGTGAGGGGGGGCCTAAAATATAATTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgc < 2:625713/151‑1 (MQ=255) aTGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgcg > 1:591856/1‑151 (MQ=255) aTGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgcg > 1:576620/1‑151 (MQ=255) ggCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGt > 1:1041473/1‑151 (MQ=255) gCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGt > 2:114962/1‑150 (MQ=255) accgggAACCCAGCGGCCAGCGTCGGGGGATGGTGGGCGTGCGGGTGGGTGATAATGGCAAAAATACCCCCGAATTGAGGGTGGGCCTAAAATAAAATTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc < 1:84322/145‑1 (MQ=255) acccggAATCCGGGGGCCAGGGTCGGGGAAATGGGGGCGTGCAGGTGGGTAATAATGCCTAAAATGACCCCGCGGTGATGGGGGGCCTAAAATAAAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACa < 2:1274/146‑1 (MQ=255) aaCCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc > 1:186413/1‑150 (MQ=255) aaCCGGAATCCGGCGGCCAGGGTCTGGGGAATGTGGGGGGGCGGTGGGGTGAAAAGGGCAAAAAGGACCCCGAAGGGAGGGGGGGCCTAAAATAAAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACa < 2:563071/151‑1 (MQ=255) ccTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat > 1:728126/1‑150 (MQ=255) cagAACCCAGCGCCCCGCGTTGGGGGAAGGTGGGCGTGCAGCTGGGTGAAAATGGCTAAAATCCCCCCGCAGGGGGGGGGGGCTTAAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc < 1:1035274/145‑1 (MQ=255) tGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg > 1:247640/1‑151 (MQ=255) aacccAGCGGCCAGCGTCGGGGGAATGTGGGCGTGCAGCGGGGTAATAATGGCTAAAATGCCCCCGCAGTGAGGGGGGGCATAAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg < 2:46798/146‑1 (MQ=255) acccAGCGGCCGGCGTCGGGGGATTGTGGGGGTTCAGCTGGATAATAAGGGCTACAACGACGCCGTATTGTTGGTGGGCATAAAATATAAG‑TCTGGCCGCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg < 1:77623/146‑1 (MQ=255) cAGTGTCGGGGTAATGTGGGCGTGCAGGTGGGTAATAATGTCTACAATGACCCCGCAGTGATGGTGGGCCTAAAATATAAGTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttttt < 1:786503/151‑1 (MQ=255) gCGTCGGGGGAATGTGGGCGTGCAGCGGGGTAAAAATGGCAACAATGACCCCGAAGGGATGGTGGGCTTAAAATATATGTTTTAATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttttt < 1:201525/149‑1 (MQ=255) tcgggggAATGTGGGCGTGCAGGGGGGTGATAATGGCTACAATGACCCCGCAGTGAGGGGGGGCCTAAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGc < 2:1041515/146‑1 (MQ=255) ggggAATGGGGGGGTGCAGCTGGGTGATAATGGCTACAATGCCCCCGCAGTGATGGTGGGCCTAAAATATAATTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttttt < 2:105207/143‑1 (MQ=255) ggggAATGGGGGCGTGCAGCTGGGTAATAAGGGCTACAATGACCCCGCGGTGAGGGGGGGCCTAAAATATAAGTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATa < 2:163237/151‑1 (MQ=255) ggggAATGGGGGCGGGCAGCGGGGTGATAAGGGCTAAAATGCCCCCGCAGTGATGGGGGGCCTAAAATATAATTTCTGCCC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt < 2:913296/144‑1 (MQ=255) aaTGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCAc > 1:523125/1‑151 (MQ=255) ggggggGTGCAGCGGGGTAATAATGTCTAAAATAACACGGGGGTGATGGGGGGCTTAAAATAAAATTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCa < 1:734389/145‑1 (MQ=255) ggggTGCAGCTGGGTAATAATGGCTACAATGCCACCGCATTGGGGGTGGGCATGAAATATATGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATgg < 1:579663/148‑1 (MQ=255) gTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt > 1:56108/1‑151 (MQ=255) gCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtc > 1:75249/1‑150 (MQ=255) gggTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAtt > 2:962050/1‑151 (MQ=255) gTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGc > 2:140970/1‑151 (MQ=255) tGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGGTC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGcc > 1:632222/1‑151 (MQ=255) aaTGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGc > 1:725653/1‑150 (MQ=255) ccgaggTGATGGGGGGCTAAAAATAAATTTTCTGTTC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCgg < 1:206961/146‑1 (MQ=255) gaaGTGGTGGGGGGCAAAAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGt < 1:823451/149‑1 (MQ=255) gCAGTGATGGTGGGCCTAAAATATAAGTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGt < 2:426710/151‑1 (MQ=255) aGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGGGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt > 2:297019/1‑151 (MQ=255) tGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt > 2:247049/1‑151 (MQ=255) ggggggCCTAAAATATAATTTCTGACC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt < 2:1033646/144‑1 (MQ=255) gtggGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgcgc > 2:555556/1‑151 (MQ=255) tggGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgcgc > 1:523766/1‑150 (MQ=255) gggCGTAAAAAATAATTTCTAATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCaa < 1:962757/151‑1 (MQ=255) gAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTg > 1:961801/1‑150 (MQ=255) | GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATC‑CCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTG > NC_000913/1222085‑1222382 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |