| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | W3110S.gb | 4,547,402 | Δ1 bp | 100% | intergenic (+87/‑395) | fimE → / → fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | W3110S.gb | 4,547,402 | 0 | T | . | 81.5% | 71.8 / 16.7 | 27 | 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 (5/0); new base . (22/0); total (27/0) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
CCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGA > W3110S.gb/4547370‑4547456 | ccAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAg > 1:3328389/1‑71 (MQ=255)ccAAACTGTCCATATCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAg > 1:1236042/1‑71 (MQ=255) tCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:1211325/1‑71 (MQ=255) tCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:3163099/1‑71 (MQ=255) tCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:3119567/1‑71 (MQ=255) tCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:2817439/1‑71 (MQ=255) tCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:1408495/1‑71 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:1258194/1‑70 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:978376/1‑70 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:893805/1‑70 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:1065572/1‑70 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGttt > 1:1886661/1‑70 (MQ=255) tCATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGtn > 1:367309/1‑68 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:2287026/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:2142091/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:1343081/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:565508/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:791440/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:807783/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:1806830/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt > 1:1758814/1‑59 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt > 1:1502242/1‑61 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa > 1:2418232/1‑71 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa > 1:3086687/1‑71 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa > 1:3261382/1‑71 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa > 1:3317303/1‑71 (MQ=255) cATAAATAAGTTACGTA‑TTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGa > 1:831315/1‑71 (MQ=255) | CCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGA > W3110S.gb/4547370‑4547456 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |