| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_004302 | 5,234 | 2 bp→GC | coding (325‑326/834 nt) | r1tp09 → | ORF9 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 5,234 | 0 | C | G | 96.9% | 153.7 / ‑2.6 | 65 | R109A (CGA→GCA) | r1tp09 | ORF9 |
| Reads supporting (aligned to +/- strand): ref base C (2/0); new base G (62/1); total (64/1) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| * | NC_004302 | 5,235 | 0 | G | C | 98.4% | 167.8 / ‑3.6 | 64 | R109A (CGA→GCA) | r1tp09 | ORF9 |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base C (62/1); total (63/1) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
CGTTAAAAAAATTACTCAACTC‑AATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACGACTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTT > NC_004302/5170‑5298 || ggtaaaaaaaaTTACTCAACTCAAATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACaagttgact > 1:11125682/5‑75 (MQ=255) gtaaatacaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTaaa > 1:4305742/8‑75 (MQ=255) gcggagaaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAAt > 1:12353659/8‑75 (MQ=255) agggaatactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATg > 1:9506892/8‑75 (MQ=255) acttttaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATg > 1:12506636/7‑75 (MQ=255) ggcctggtc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGaa > 1:3188328/8‑75 (MQ=255) tcaaactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAg > 1:16516111/4‑75 (MQ=255) agtcactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAg > 1:11542206/5‑75 (MQ=255) gctactc‑atTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:727811/4‑75 (MQ=255) cagactc‑aaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:6150945/4‑75 (MQ=255) tagtaagaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:14358604/8‑75 (MQ=255) gtgtaaaaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:3042486/8‑75 (MQ=255) cctggggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:1513639/8‑75 (MQ=255) cctggggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGc > 1:11440373/8‑75 (MQ=255) tagggggaTAGTGATTATGACGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGACGCt > 1:913612/8‑75 (MQ=255) tagggggaTAGTGATTATGACGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGACGCt > 1:12117749/8‑75 (MQ=255) tgctaaataatGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa > 1:9320870/6‑75 (MQ=255) gcttccttAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa > 1:4685281/8‑75 (MQ=255) gcttccttAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa > 1:10019461/8‑75 (MQ=255) cctaataTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa > 1:1911903/7‑75 (MQ=255) actttaaTAGGGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTa > 1:11148269/6‑75 (MQ=255) catattgaGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa > 1:12127715/8‑75 (MQ=255) catattgaGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa > 1:17139487/8‑75 (MQ=255) atc‑aaTAGTGATTATGATGAACGCAGACGA‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAAt > 1:16678326/2‑75 (MQ=255) aaggaaTAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTaa > 1:16356460/5‑75 (MQ=255) actatatgTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAAt > 1:3898888/8‑75 (MQ=255) taagtgTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGt > 1:2523448/6‑75 (MQ=255) ggtaaGTGA‑TATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTa > 1:5993510/5‑75 (MQ=255) gcatagATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAg > 1:3268353/6‑75 (MQ=255) ccaatcttATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGt > 1:11347226/7‑75 (MQ=255) aaaggATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGt > 1:1633280/5‑75 (MQ=255) ttGATTATAATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGttt > 1:4680211/2‑75 (MQ=255) gggatATGATGCACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTa > 1:2971737/5‑75 (MQ=255) ttcaatgaagAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGGAAATGAAGCTAATGTAGTTTAt > 1:14397658/5‑75 (MQ=255) cgagggttgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATg > 1:16256001/8‑75 (MQ=255) aTTATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATg > 1:15648946/1‑75 (MQ=255) atatagtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATgg > 1:10162370/7‑75 (MQ=255) ttcgaagaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg > 1:5193779/7‑75 (MQ=255) tATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg > 1:1494027/1‑75 (MQ=255) tATGATGAACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg < 1:1269944/75‑1 (MQ=255) taagtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGc > 1:3729874/5‑75 (MQ=255) attatacaCGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGc > 1:8599473/8‑75 (MQ=255) gtgaACGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCttt > 1:15269382/2‑75 (MQ=255) cgtaaCGCAGACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCttt > 1:12047984/4‑75 (MQ=255) tttatttgACGG‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt > 1:2750890/8‑75 (MQ=255) acgcGCAGACGGAAAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTc > 1:3947649/4‑75 (MQ=255) agaagaggg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgt > 1:13575822/8‑75 (MQ=255) gtggtaag‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgta > 1:4346066/8‑75 (MQ=255) gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag > 1:12223935/7‑75 (MQ=255) gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag > 1:10984602/7‑75 (MQ=255) gctatagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGC‑TTCTGgtag > 1:11004865/7‑75 (MQ=255) acatgttg‑AAAACAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgta > 1:11291704/8‑75 (MQ=255) ctcgagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtag > 1:10934604/6‑75 (MQ=255) cgctagg‑AATGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtag > 1:12038132/6‑75 (MQ=255) atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta > 1:12795405/4‑75 (MQ=255) atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta > 1:7275243/4‑75 (MQ=255) atagg‑AAAGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta > 1:11269103/4‑75 (MQ=255) gaagaaaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagat > 1:15445413/6‑73 (MQ=255) aactcaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAACTAATGTAGTTTATGGGCTTTCTGGtagtag > 1:15870132/6‑75 (MQ=255) tgagaaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGa > 1:15262937/5‑75 (MQ=255) ccttactcAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGa > 1:4997243/8‑75 (MQ=255) ggtgaGCAGGATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAt > 1:1269347/5‑75 (MQ=255) gcaaGCAGAATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAtt > 1:4878662/3‑75 (MQ=255) gagggATTTGAAGCAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCt > 1:16281584/4‑75 (MQ=255) tgaggctGAACGAGTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCttt > 1:4538497/7‑75 (MQ=255) || CGTTAAAAAAATTACTCAACTC‑AATAGTGATTATGATGAACGCAGACGG‑AAAGCAGGATTTGAACGACTTGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTT > NC_004302/5170‑5298 |
| 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: ‑ |