| Variant ID: vg0804463814 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463814 |
| 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: 94. )
TAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTT[G/A]
AAAATTTATATCCCAATAGGTTCTATGAATATCATACTATTTATAAGATTTTATTTGATTTTTTCCTTTTTTATCAATTTAAATTTGAATTTGGATGAAA
TTTCATCCAAATTCAAATTTAAATTGATAAAAAAGGAAAAAATCAAATAAAATCTTATAAATAGTATGATATTCATAGAACCTATTGGGATATAAATTTT[C/T]
AAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTA
| 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 | 34.60% | 0.90% | 0.91% | 63.63% | NA |
| All Indica | 2759 | 5.00% | 1.50% | 0.72% | 92.82% | NA |
| All Japonica | 1512 | 94.90% | 0.00% | 0.20% | 4.89% | NA |
| Aus | 269 | 3.30% | 0.00% | 5.58% | 91.08% | NA |
| Indica I | 595 | 6.70% | 2.70% | 1.34% | 89.24% | NA |
| Indica II | 465 | 6.20% | 1.90% | 0.65% | 91.18% | NA |
| Indica III | 913 | 2.50% | 0.50% | 0.00% | 96.93% | NA |
| Indica Intermediate | 786 | 5.70% | 1.40% | 1.15% | 91.73% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.26% | 1.56% | NA |
| Tropical Japonica | 504 | 88.70% | 0.00% | 0.00% | 11.31% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 3.12% | 80.21% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 2.22% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463814 | G -> A | LOC_Os08g07900.1 | upstream_gene_variant ; 3591.0bp to feature; MODIFIER | silent_mutation | Average:14.8; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463814 | G -> A | LOC_Os08g07910.1 | upstream_gene_variant ; 2693.0bp to feature; MODIFIER | silent_mutation | Average:14.8; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463814 | G -> A | LOC_Os08g07930.1 | upstream_gene_variant ; 2215.0bp to feature; MODIFIER | silent_mutation | Average:14.8; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463814 | G -> A | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.8; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463814 | G -> DEL | N | N | silent_mutation | Average:14.8; most accessible tissue: Callus, score: 29.336 | N | N | N | N |