| Variant ID: vg0219101129 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19101129 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, G: 0.13, others allele: 0.00, population size: 250. )
ACCTTGAGAATTTCCTTTTGTTTGGATTCAGATGCAGATCCATTGGAAACTTCTTCACCCTCTACATAATTCTCCCAGATCTTGAAAAAGAAAAGGATGT[C/G]
AGCATGTTTTCTCCTTGTGTAGTTCAAGAATAGAAGTGGTTACCTTGAGTTTCTGCTGCTTTGCAGACTGTTCAGCCCTCATTAGAACATTTGCATCCGG
CCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGGTAACCACTTCTATTCTTGAACTACACAAGGAGAAAACATGCT[G/C]
ACATCCTTTTCTTTTTCAAGATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 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 | 76.60% | 23.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.30% | 9.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0219101129 | C -> G | LOC_Os02g32340.1 | upstream_gene_variant ; 3713.0bp to feature; MODIFIER | silent_mutation | Average:65.946; most accessible tissue: Zhenshan97 flower, score: 81.724 | N | N | N | N |
| vg0219101129 | C -> G | LOC_Os02g32350.1 | intron_variant ; MODIFIER | silent_mutation | Average:65.946; most accessible tissue: Zhenshan97 flower, score: 81.724 | N | N | N | N |
| vg0219101129 | C -> G | LOC_Os02g32350.2 | intron_variant ; MODIFIER | silent_mutation | Average:65.946; most accessible tissue: Zhenshan97 flower, score: 81.724 | N | N | N | N |