| Variant ID: vg0200790862 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 790862 |
| 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, A: 0.01, others allele: 0.00, population size: 295. )
TGGCCTAAGAATTGTGATCAAGCTAAGCTTGAACTAACCCAAAGCTAAGTACTCTCTGTAACTGCTAATTACCAATTAGAGAGGGGACTAGACTAGGCTA[G/A]
AATTCACAATTGTGAAGAGGGATGCATTGGTGAATGCAGCAATGTGCATTCACAGTAGAGACAGAGAGAAGCAAAAAGCTCACCAGCCTTTGCAGGGACA
TGTCCCTGCAAAGGCTGGTGAGCTTTTTGCTTCTCTCTGTCTCTACTGTGAATGCACATTGCTGCATTCACCAATGCATCCCTCTTCACAATTGTGAATT[C/T]
TAGCCTAGTCTAGTCCCCTCTCTAATTGGTAATTAGCAGTTACAGAGAGTACTTAGCTTTGGGTTAGTTCAAGCTTAGCTTGATCACAATTCTTAGGCCA
| 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 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 60.60% | 39.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 91.30% | 8.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.40% | 6.60% | 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 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200790862 | G -> A | LOC_Os02g02360.1 | downstream_gene_variant ; 1627.0bp to feature; MODIFIER | silent_mutation | Average:67.919; most accessible tissue: Zhenshan97 root, score: 81.772 | N | N | N | N |
| vg0200790862 | G -> A | LOC_Os02g02380.1 | downstream_gene_variant ; 4204.0bp to feature; MODIFIER | silent_mutation | Average:67.919; most accessible tissue: Zhenshan97 root, score: 81.772 | N | N | N | N |
| vg0200790862 | G -> A | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.919; most accessible tissue: Zhenshan97 root, score: 81.772 | N | N | N | N |