| Variant ID: vg0826583961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26583961 |
| 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: 327. )
CGAAGATTTCTTTGACACTTACTCACCTGTTGCTAGATTGACCACAATTCGTGTGCTACTTTCCCTAGCAGCCTCACATGGTCTTCTCGTTCATCAAATG[G/A]
ACGTTAAGACAGCTTTTCTTAATGGAGAGCTGGATGAGGAGATCTATATGGATCAACCTGATGGGTTTGTAGTTGAAGGTCAAGAAGGCAAAGTGTGCAA
TTGCACACTTTGCCTTCTTGACCTTCAACTACAAACCCATCAGGTTGATCCATATAGATCTCCTCATCCAGCTCTCCATTAAGAAAAGCTGTCTTAACGT[C/T]
CATTTGATGAACGAGAAGACCATGTGAGGCTGCTAGGGAAAGTAGCACACGAATTGTGGTCAATCTAGCAACAGGTGAGTAAGTGTCAAAGAAATCTTCG
| 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 | 30.40% | 0.40% | 24.23% | 44.92% | NA |
| All Indica | 2759 | 1.90% | 0.70% | 36.90% | 60.49% | NA |
| All Japonica | 1512 | 81.40% | 0.00% | 1.65% | 16.93% | NA |
| Aus | 269 | 9.70% | 0.00% | 29.37% | 60.97% | NA |
| Indica I | 595 | 0.50% | 0.70% | 27.06% | 71.76% | NA |
| Indica II | 465 | 2.40% | 0.00% | 21.51% | 76.13% | NA |
| Indica III | 913 | 1.20% | 1.40% | 53.12% | 44.25% | NA |
| Indica Intermediate | 786 | 3.40% | 0.40% | 34.61% | 61.58% | NA |
| Temperate Japonica | 767 | 94.80% | 0.00% | 0.52% | 4.69% | NA |
| Tropical Japonica | 504 | 70.40% | 0.00% | 2.78% | 26.79% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 2.90% | 35.27% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 3.12% | 3.12% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 22.22% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826583961 | G -> A | LOC_Os08g42090.1 | missense_variant ; p.Asp902Asn; MODERATE | nonsynonymous_codon ; D902N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0826583961 | G -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |