| Variant ID: vg0202540208 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2540208 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 245. )
GAGTAATTGGTAGATTGGTTTTTTAAATTAATCTACTAATTTCGTAGATACATCCGGCATGTATCTACAAAGGTACGCAATATTTTATATGCAATTTATC[A/G]
TACCTATTCAGATCATACAGAATTGTCAGATCTATAATTTATTATGTTTACCTAGAGCATGTCTTTTATACAATATCTATTGCACGAGTATTTCCGACGT
ACGTCGGAAATACTCGTGCAATAGATATTGTATAAAAGACATGCTCTAGGTAAACATAATAAATTATAGATCTGACAATTCTGTATGATCTGAATAGGTA[T/C]
GATAAATTGCATATAAAATATTGCGTACCTTTGTAGATACATGCCGGATGTATCTACGAAATTAGTAGATTAATTTAAAAAACCAATCTACCAATTACTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 4.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 96.80% | 3.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 5.20% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540208 | A -> G | LOC_Os02g05270.1 | upstream_gene_variant ; 4033.0bp to feature; MODIFIER | silent_mutation | Average:37.908; most accessible tissue: Zhenshan97 flower, score: 45.926 | N | N | N | N |
| vg0202540208 | A -> G | LOC_Os02g05280.1 | downstream_gene_variant ; 1538.0bp to feature; MODIFIER | silent_mutation | Average:37.908; most accessible tissue: Zhenshan97 flower, score: 45.926 | N | N | N | N |
| vg0202540208 | A -> G | LOC_Os02g05300.1 | downstream_gene_variant ; 1882.0bp to feature; MODIFIER | silent_mutation | Average:37.908; most accessible tissue: Zhenshan97 flower, score: 45.926 | N | N | N | N |
| vg0202540208 | A -> G | LOC_Os02g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.908; most accessible tissue: Zhenshan97 flower, score: 45.926 | N | N | N | N |