| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,222,233 | 0 | G | A | 41.9% | 31.9 / 18.0 | 32 | pseudogene (60/75 nt) | ycgH | pseudogene; putative ATP‑binding component of a transport system |
| Reads supporting (aligned to +/- strand): ref base G (17/1); new base A (0/13); total (17/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.79e-08 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
GTGTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGC > NC_000913/1222083‑1222373 | gtgtGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTg < 1:326302/151‑1 (MQ=255) aaGCTGGGGCGAGTAATTGGGGGGAAATTAAACTTGGCGTAAATGGAAACCTGAATACAGCGGCCAGCGTATGGGGAATGGGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGGAGTGATGTTGGGCCTGAAATATAA‑Gtt > 1:458/1‑147 (MQ=255) aTGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATcc > 1:245561/1‑151 (MQ=255) gAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGtt > 1:614166/1‑151 (MQ=255) aTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCt > 2:384101/1‑150 (MQ=255) tttGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTa > 2:86865/1‑150 (MQ=255) gggAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAAc > 1:142815/1‑151 (MQ=255) aaTTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACcgcg > 2:644708/1‑151 (MQ=255) aaaCTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcgt > 1:476354/1‑151 (MQ=255) aaCTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGGGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcgt > 1:355812/1‑150 (MQ=255) ccTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat > 1:506223/1‑150 (MQ=255) gAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACCATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg > 1:18818/1‑150 (MQ=255) aagccggcggcgggggTCTGGGAAATGTGGGCGTGCAGGTGGGTT‑ATAATGGCTACAATGACACCGCAGTTATGGTGGGCTTAAAATATAA‑TTTCAGCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa < 2:239184/136‑1 (MQ=255) aacccAGCGGCAGGGGTCGGGGAAAGGGGGGGGGGCAGCGGGGTA‑ATAATGCCTAAAAGGCCCCCGCAGTGATGGGGGGCTTAAAATAAAG‑TTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat < 1:366124/143‑1 (MQ=255) cccgCGGCCAGCTTGGGGGGAATGGGGGCGTGGCGGTGGGGG‑AAAATGCCTACAAACACCCCGCAGTGGTGGGGGGCCAAAAATTTAA‑TTTCTTCCCCCCCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg < 2:225980/143‑1 (MQ=255) ccggCGTCTGGGGAAGGGGGGCGTGCAGTTGGGTA‑AAAATGGCTACAAGAACCCCGCAGTGTGGGGGGTCAAAAAATATAA‑GTTCTACCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt < 2:229430/148‑1 (MQ=255) ccAGCGTCTGGGGAATGGGGGGGTGCAGTTGGGTA‑ATAATGGCTACAATGACCCCGCAGTGATGGTGGGCCTAAAATATAA‑TTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtatta < 2:457966/147‑1 (MQ=255) cGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGc > 2:470915/1‑151 (MQ=255) gggggatggggggcgggcAGGTGGGTA‑ATAATGGCTAAAATGACCCCGCAGTGAGGGGGGGCCTAAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt < 1:237033/141‑1 (MQ=255) ggggAATGGGGGCGTGGAG‑TGGGTGTATAGTGGCTACAATGACCCCGAATGGGTGGTGGCCCAAAAATAAAT‑TTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCg < 1:680001/148‑1 (MQ=255) ggATTGTGGGGGTGCCGCGGGGTG‑ATAGGGGCTACAATACCCCCGCGGTGAGGGTGGGCTGAAAATATAT‑TTCCTAACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGc < 1:689442/151‑1 (MQ=255) gggggtgagggggggTG‑ATAGTGGCTAAAAGGACCCCGCGGTGAGGGGGGGCCTAAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGc < 2:192797/132‑1 (MQ=255) ggcggTGCAGCTGGGTG‑ATAATGGTTAAAATGACACCGCTGTGATGGTGGGCTAAAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATg < 1:795391/147‑1 (MQ=255) gTGCAGCTGGGGA‑ATATTGATTACAAGACCACCGAAGTGGGGGTGTGCCTAAAATATAT‑TTCCTCACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgt < 2:211581/149‑1 (MQ=255) tAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTg > 1:125895/1‑151 (MQ=255) tGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATc > 2:695499/1‑151 (MQ=255) tACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAAc > 1:420858/1‑150 (MQ=255) tACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAAc > 2:556094/1‑150 (MQ=255) aCAACGACACCGGGGTGATGGTGGCACTGAAATATAA‑TTTCTAGTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCaa < 2:658191/148‑1 (MQ=255) gtaGTGGTGGTGGACGTAAAATAAAA‑GTTCTGAGCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCg < 2:451521/146‑1 (MQ=255) tGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt > 2:329173/1‑151 (MQ=255) ggggggCATAAAAAATAG‑TTTCTTACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgc < 1:334823/147‑1 (MQ=255) ggggCGTTAAATATAATGTTCGGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGt < 1:41713/141‑1 (MQ=255) | GTGTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTG‑ATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAA‑GTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGC > NC_000913/1222083‑1222373 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |