| Variant ID: vg0804463706 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463706 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 107. )
AAACCAAAATTTGAATACAAATTCTCTGAGTTTACCGATAAGCTTGTGAAAACCGGTCGGCTTTGGCGAAATTCCGAGCGAAATCATCGAAATTTCAATC[A/C]
ATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAG
CTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTAT[T/G]
GATTGAAATTTCGATGATTTCGCTCGGAATTTCGCCAAAGCCGACCGGTTTTCACAAGCTTATCGGTAAACTCAGAGAATTTGTATTCAAATTTTGGTTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.20% | 0.60% | 0.51% | 64.66% | NA |
| All Indica | 2759 | 4.50% | 0.40% | 0.43% | 94.64% | NA |
| All Japonica | 1512 | 95.00% | 0.20% | 0.07% | 4.70% | NA |
| Aus | 269 | 1.90% | 4.50% | 3.35% | 90.33% | NA |
| Indica I | 595 | 6.70% | 0.00% | 0.50% | 92.77% | NA |
| Indica II | 465 | 6.00% | 0.00% | 0.22% | 93.76% | NA |
| Indica III | 913 | 1.80% | 0.70% | 0.11% | 97.48% | NA |
| Indica Intermediate | 786 | 5.20% | 0.60% | 0.89% | 93.26% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 88.70% | 0.60% | 0.00% | 10.71% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 1.04% | 82.29% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 1.11% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463706 | A -> C | LOC_Os08g07900.1 | upstream_gene_variant ; 3483.0bp to feature; MODIFIER | silent_mutation | Average:14.334; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463706 | A -> C | LOC_Os08g07910.1 | upstream_gene_variant ; 2585.0bp to feature; MODIFIER | silent_mutation | Average:14.334; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463706 | A -> C | LOC_Os08g07930.1 | upstream_gene_variant ; 2323.0bp to feature; MODIFIER | silent_mutation | Average:14.334; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463706 | A -> C | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.334; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463706 | A -> DEL | N | N | silent_mutation | Average:14.334; most accessible tissue: Callus, score: 29.336 | N | N | N | N |