| Variant ID: vg0826584564 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584564 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 96. )
CAAGAACAAGAGAATTGCTAGAAATCAACTGGAATACTCCCAAATCATTGGCTCGTTGATGTACCTGGCTAGTGCAACTAGGCCTGATATCTCCTTTGCT[G/A]
TGAGCAAGTTGAGCCGATTTACCTCTAATCCGGGAGATGATCACTGGCGTGCACTTGAGCGAGTAATGCGCTATCTGAAAGGTACTGTGGAATTGGGGCT
AGCCCCAATTCCACAGTACCTTTCAGATAGCGCATTACTCGCTCAAGTGCACGCCAGTGATCATCTCCCGGATTAGAGGTAAATCGGCTCAACTTGCTCA[C/T]
AGCAAAGGAGATATCAGGCCTAGTTGCACTAGCCAGGTACATCAACGAGCCAATGATTTGGGAGTATTCCAGTTGATTTCTAGCAATTCTCTTGTTCTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.60% | 0.10% | 25.12% | 74.19% | NA |
| All Indica | 2759 | 0.50% | 0.20% | 18.30% | 80.97% | NA |
| All Japonica | 1512 | 0.80% | 0.00% | 34.72% | 64.48% | NA |
| Aus | 269 | 0.00% | 0.00% | 21.56% | 78.44% | NA |
| Indica I | 595 | 1.80% | 0.20% | 14.62% | 83.36% | NA |
| Indica II | 465 | 0.00% | 0.00% | 11.40% | 88.60% | NA |
| Indica III | 913 | 0.00% | 0.30% | 26.07% | 73.60% | NA |
| Indica Intermediate | 786 | 0.50% | 0.10% | 16.16% | 83.21% | NA |
| Temperate Japonica | 767 | 1.00% | 0.00% | 29.99% | 68.97% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 44.05% | 55.36% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 30.29% | 69.29% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 76.04% | 22.92% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 28.89% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584564 | G -> A | LOC_Os08g42090.1 | missense_variant ; p.Val1103Met; MODERATE | nonsynonymous_codon ; V1103M | Average:11.359; most accessible tissue: Minghui63 panicle, score: 20.733 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0826584564 | G -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:11.359; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |