| Variant ID: vg0817015804 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015804 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTGCACTACCACAAGGTGTCAATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACA[G/C]
CAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCC
GGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTG[C/G]
TGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCATTGACACCTTGTGGTAGTGCAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.60% | 0.10% | 25.22% | 50.08% | NA |
| All Indica | 2759 | 10.90% | 0.00% | 27.84% | 61.29% | NA |
| All Japonica | 1512 | 51.00% | 0.30% | 15.61% | 33.13% | NA |
| Aus | 269 | 19.30% | 0.00% | 37.55% | 43.12% | NA |
| Indica I | 595 | 7.10% | 0.00% | 10.25% | 82.69% | NA |
| Indica II | 465 | 2.40% | 0.00% | 26.45% | 71.18% | NA |
| Indica III | 913 | 18.70% | 0.00% | 40.20% | 41.07% | NA |
| Indica Intermediate | 786 | 9.70% | 0.00% | 27.61% | 62.72% | NA |
| Temperate Japonica | 767 | 70.30% | 0.00% | 10.56% | 19.17% | NA |
| Tropical Japonica | 504 | 26.80% | 0.00% | 18.25% | 54.96% | NA |
| Japonica Intermediate | 241 | 40.20% | 1.70% | 26.14% | 31.95% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 67.71% | 20.83% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 24.44% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015804 | G -> C | LOC_Os08g27910.1 | missense_variant ; p.Gln404His; MODERATE | nonsynonymous_codon ; Q404H | Average:5.77; most accessible tissue: Callus, score: 12.96 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0817015804 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.77; most accessible tissue: Callus, score: 12.96 | N | N | N | N |