| 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 | 92.9% | 64.5 / ‑0.3 | 28 | R109A (CGA→GCA) | r1tp09 | ORF9 |
| Reads supporting (aligned to +/- strand): ref base C (2/0); new base G (25/1); total (27/1) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 | |||||||||||
| * | NC_004302 | 5,235 | 0 | G | C | 92.9% | 66.7 / ‑0.9 | 29 | R109A (CGA→GCA) | r1tp09 | ORF9 |
| Reads supporting (aligned to +/- strand): ref base G (1/0); major base C (25/1); minor base A (2/0); total (28/1) | |||||||||||
| 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 | |||||||||||
TTAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑CGACTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTAACA > NC_004302/5172‑5302 || gtAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAg > 1:4098499/2‑75 (MQ=255)gtAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAg > 1:17006994/2‑75 (MQ=255) tgttgagtcaactcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTaa > 1:9869790/8‑75 (MQ=255) taaatatactcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATg > 1:16779127/8‑75 (MQ=255) cgagatctcaaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGAAGTAAATGaa > 1:8076379/7‑75 (MQ=255) tggttttAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTaa > 1:6610009/7‑75 (MQ=255) ggatcgtAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAAGCAGTTT‑GACTTAGCAGTAAATGAAGCTa > 1:16454581/7‑75 (MQ=255) ggatcgtAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAAGCAGTTT‑GACTTAGCAGTAAATGAAGCTa > 1:6873848/7‑75 (MQ=255) ggaagaGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATg > 1:14583510/6‑75 (MQ=255) tgctgatGATTCTGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGt > 1:315741/7‑75 (MQ=255) caaTAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGcaagatc > 1:1753292/1‑69 (MQ=255) aggtgagttATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAg > 1:12447066/8‑75 (MQ=255) cggccgatATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGt > 1:13330801/8‑75 (MQ=255) aatccgttATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGt > 1:3128087/7‑75 (MQ=255) gcagATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtt > 1:8869797/4‑75 (MQ=255) gagaatcatgatgAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtt > 1:16310036/8‑75 (MQ=255) agggttttgaATGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATg > 1:2962984/8‑75 (MQ=255) ctgctatgaACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATgg > 1:6747262/6‑75 (MQ=255) tATGATGAACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGtcttttat < 1:2453427/75‑8 (MQ=255) actagtgaACGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATggg > 1:481304/6‑75 (MQ=255) tttttttgCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCtt > 1:5006996/8‑75 (MQ=255) cgtagCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt > 1:16559602/5‑75 (MQ=255) ataCGCAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt > 1:2118373/3‑75 (MQ=255) agaatcAGACGGAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCt > 1:1079053/6‑75 (MQ=255) gacacgAAAGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagt > 1:15783342/6‑75 (MQ=255) gcatgtgaGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGgtagta > 1:5406262/8‑75 (MQ=255) caggataaGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGAt > 1:12250339/8‑75 (MQ=255) aaGCAGGATTTGAA‑GCAGTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTg > 1:63029/1‑75 (MQ=255) gtcttcGACTTAGACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTaaca > 1:5123467/6‑75 (MQ=255) || TTAAAAAAATTACTCAACTCAATAGTGATTATGATGAACGCAGACGGAAAGCAGGATTTGAA‑CGACTT‑GACTTAGCAGTAAATGAAGCTAATGTAGTTTATGGGCTTTCTGGTAGTAGATTTGCTTTAACA > NC_004302/5172‑5302 |
| 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: ‑ |