| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,222,233 | 0 | G | A | 38.6% | 61.3 / 15.3 | 44 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| Reads supporting (aligned to +/- strand): ref base G (21/6); new base A (0/17); total (21/23) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.56e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
GAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGC > NC_000913/1222094‑1222373 | gAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGtt > 1:859952/1‑151 (MQ=255) cAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTg > 1:793204/1‑151 (MQ=255) ggggCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCccg < 2:472500/151‑1 (MQ=255) ggggCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCccg < 1:695151/151‑1 (MQ=255) ggggCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCccg < 1:480754/151‑1 (MQ=255) gCGAGTATTTTGGGGGAAATTAAACTTGGCGTAAATGGCACCCTGAATCCAGCGGCCAGGGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCccgccg < 1:600782/151‑1 (MQ=255) aaTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCt > 1:580173/1‑151 (MQ=255) aTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCt > 1:623973/1‑150 (MQ=255) gAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACcg > 2:950189/1‑151 (MQ=255) aacctgggCGAAAAGGGCACCCTGAACCCAGCGGCCGGTGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGCCCCCGCAGTGATGGTGGGCCTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGcgtc < 1:529900/143‑1 (MQ=255) aCTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTAt > 1:549711/1‑151 (MQ=255) ggggaaaaggccacccTAAACCCAGGGCCCGGCGTGGGGGAAATGGGGGGGTGCGGTTGGGTGA‑AAAGGCTAACAATCACCCCGCAGTGAGGGGGGTCTTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCAt < 1:609672/137‑1 (MQ=255) ggCGTAAATGGCACCCTAAACCCAGCGCCCGGCGTCTGGGGATTGTGGGCGTGCAGCGGGGTGATAATGGCT‑AAAATGACCCCGCGGTGATGGTGGGCCTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTAt < 1:132654/147‑1 (MQ=255) aaaTGGCAACCTGAACCCAGCGGCCAGCGTCGGGGAAATGGGGGGGTGCAGCTGGGTGATAATGGCT‑ACAATGACCCCGCAGTGAGGGTGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg < 1:511624/148‑1 (MQ=255) gCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCTTCGTATTCATCGACGCgg > 2:241882/1‑149 (MQ=255) cgtGAACCCAGCGGCCAGCGTCGGGGGAATGGGGGGGTGCAGCTGGGTGATAATGGCA‑ACAATGACCCCGCAGTGATGGTGGGCTTAAAATATAAGTTCTTATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc < 1:249044/146‑1 (MQ=255) ccggAATCCGGCGGCCGGCTTCGGGGGAAGGGGGGCTTGCAGCTGGTTGATAATGGCT‑ACAATGACCCCGAAGTGATGGTGGGCCTAAAATATAGGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat < 2:132384/147‑1 (MQ=255) ccTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat > 1:733154/1‑150 (MQ=255) ccTAAATCCGGCGGCCGGCGTCGGGGAAATGTGGGCGTGCAGCTGGGTAATAATGGCT‑ACAATGCCCCCGCAGTGATGGTGGGCTTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat < 1:516634/150‑1 (MQ=255) tGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg > 2:119615/1‑151 (MQ=255) aaTCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGa > 1:878995/1‑150 (MQ=255) aaTCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGa > 2:576303/1‑150 (MQ=255) ccAGCGGCCAGGTTCGGGGGAAGGGGGGCGTGCAGGTGGGTGATAATGGCT‑ACAATGCCCCCGCAGTTATGGTGGGCTAAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaaa < 2:810432/149‑1 (MQ=255) ccAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTACAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAat > 2:878959/1‑150 (MQ=255) cggCGTCGGGGGAATGGGGGGGTGCGGTTGGGTAATAATGGCT‑ACAATGACCCCGCGGTGATGGTGGGCTTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATAAAATATTAttttt < 1:940116/149‑1 (MQ=255) ggggTCGGGGGATGGGGGGTGTGCGGGTGGGTAAAAATGTCA‑AAAAGGACCCAGAAGGTAGGGTGGCCCTAAAATATAGTTTCGGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt < 2:521752/148‑1 (MQ=255) gTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGcc > 2:45360/1‑151 (MQ=255) gtgGGCGTGCAGGTGGGTAATAATGGCT‑AAAATGACCCCGGAGTGATGGTGGGCTTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCa < 1:821111/147‑1 (MQ=255) ggggggGTGCAGTTGGGGGATAATGGCT‑AAAATGACCCCGCAGGGATGGTGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACg < 1:885234/147‑1 (MQ=255) cGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtg > 1:361938/1‑151 (MQ=255) tGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAt > 2:770708/1‑151 (MQ=255) gggTGATAAGGGCT‑AAAATGACCCCGAGGTGAGGGGGGGCTGAAAAAATAATTTCTAATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtca < 2:443123/145‑1 (MQ=255) gggAGATAAGGGTT‑AAAATGACACCGCAGTGGTGGTGGGTCTAAAATATAATTTCTGGTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtc < 2:536441/144‑1 (MQ=255) gATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCg > 2:110635/1‑151 (MQ=255) ctccAATCACCCCGCAGTGATGGTGGGCCTGAAATATAAGTTCTCATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCaa < 2:202063/147‑1 (MQ=255) aaggACCCCGCAGTGATGGTGGGCCAAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCa < 1:906637/148‑1 (MQ=255) accggggggATGGCGGGCCTGAAATAGAAGTTCAGTTACCGCCGTTAGCTAAAAAGCCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCg < 2:303694/143‑1 (MQ=255) gCAGTGATGGTGGGCCTGAAATATAAATTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGCATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGt > 1:410667/1‑151 (MQ=255) cAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTc > 2:468078/1‑151 (MQ=255) cAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTc > 1:506552/1‑151 (MQ=255) gtgaggtggggCATAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt < 2:101055/142‑1 (MQ=255) tGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt > 2:140451/1‑151 (MQ=255) tggtggGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgc > 1:203392/1‑151 (MQ=255) ggtggGCCTAAAATATAGTTTCGGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgc < 1:45372/150‑1 (MQ=255) | GAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCT‑ACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGC > NC_000913/1222094‑1222373 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |