| Variant ID: vg1202831643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2831643 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 295. )
GATTGAGGCGAAAGGCAAGATTCATGTTTTTGTTGCTGGAGAGAGAGAACACCCAGGAATAACTGATGTATACAATAAGTTGGAGGAAATTTACCATGAG[A/T]
TGAGAAAGATTTCTCACAGAGCCAACACACAATGTGATCTGCATGATGTGCATGCTGACCAAAAAGAGGAGCTACTTAAACACCACAGTGAGAAACTAGC
GCTAGTTTCTCACTGTGGTGTTTAAGTAGCTCCTCTTTTTGGTCAGCATGCACATCATGCAGATCACATTGTGTGTTGGCTCTGTGAGAAATCTTTCTCA[T/A]
CTCATGGTAAATTTCCTCCAACTTATTGTATACATCAGTTATTCCTGGGTGTTCTCTCTCTCCAGCAACAAAAACATGAATCTTGCCTTTCGCCTCAATC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1202831643 | A -> T | LOC_Os12g06070.1 | missense_variant ; p.Met534Leu; MODERATE | N | Average:53.567; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | N | N | N | N |
| vg1202831643 | A -> T | LOC_Os12g06080.1 | downstream_gene_variant ; 4378.0bp to feature; MODIFIER | N | Average:53.567; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | N | N | N | N |