| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | W3110S.gb | 4,547,402 | 0 | T | . | 48.0% | 66.0 / 95.2 | 50 | intergenic (+87/‑395) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| Reads supporting (aligned to +/- strand): ref base T (15/11); new base . (6/18); total (21/29) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.46e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATT > W3110S.gb/4547343‑4547466 | ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAg < 1:2404493‑M1/49‑1 (MQ=255)ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAg < 1:3255439‑M1/49‑1 (MQ=255)ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAg < 1:2920393‑M1/49‑1 (MQ=255)ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAg < 1:3672637‑M1/49‑1 (MQ=255)ttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAg < 1:2873762‑M1/49‑1 (MQ=255) ccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATaaa > 1:3647927‑M1/17‑71 (MQ=255) ccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATaaa > 1:3477478‑M1/17‑71 (MQ=255) gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAatat < 1:2252231‑M1/60‑1 (MQ=255) gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAatat < 1:1229338‑M1/60‑1 (MQ=255) gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAatat < 1:446991‑M1/60‑1 (MQ=255) gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAatat < 1:1435210‑M1/60‑1 (MQ=255) gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAatat < 1:2043137‑M1/60‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:2348093/71‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:2102949/71‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:3278071/71‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:1666254/71‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:3163193/71‑1 (MQ=255) aGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:1226158/71‑1 (MQ=255) cAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAAc < 1:2352638/71‑1 (MQ=255) cAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAAc < 1:2232642/71‑1 (MQ=255) cAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAAc < 1:2347866/71‑1 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:2017957‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:2727548‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:2770986‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:103392‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:3558338‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:1993848‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:1863836‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:1822511‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:165162‑M1/1‑71 (MQ=255) GGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGCATAAAAATATTAAAAAACGACaaa > 1:3055943‑M1/1‑71 (MQ=255) GCCAAACTGTCCATATCATAAATAAGTTACGTATTTTT‑CTCAAGc < 1:2773550‑M1/45‑1 (MQ=255) aCTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTaaaa < 1:3098608/55‑1 (MQ=255) cTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATc > 1:305678/1‑70 (MQ=255) cTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATc > 1:3075174/1‑70 (MQ=255) cTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt < 1:518450/71‑1 (MQ=255) cTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt < 1:2978363/71‑1 (MQ=255) cTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt < 1:2670382/71‑1 (MQ=255) ccATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt < 1:97769/67‑1 (MQ=255) atatCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt < 1:3138446/65‑1 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:3173126/1‑70 (MQ=255) ataaataaGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa < 1:3345059/70‑1 (MQ=255) ataaataaGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa < 1:1316808/70‑1 (MQ=255) ataaataaGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACAACAAAAAGCATCTAACTGTTTGa > 1:2008720/1‑70 (MQ=255) aaataaGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata > 1:1948701/1‑71 (MQ=255) aaataaGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata > 1:4071364/1‑71 (MQ=255) aaataaGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGata > 1:3054509/1‑71 (MQ=255) taaGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGt > 1:2965475/1‑70 (MQ=255) taaGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGt > 1:1966911/1‑70 (MQ=255) ttACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt < 1:2802275/71‑1 (MQ=255) | AAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATT > W3110S.gb/4547343‑4547466 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |