| Variant ID: vg0228079723 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28079723 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 295. )
TGCAAAAATAACAAATTGATCTTGCAGAGAAAGAACTCTTGTGCAGATAGATGGCTCTGCTGTTAGAACAGGTCGGCGAAGAGGCTCAGAAAGGCGGAAG[C/T]
GAGTTATGGATGGATCAAGAGCAAATTCACGCCTCTTTAAATATGCATCACCTATAGTCCTTGAAACCTGGTAAGTAATCACAAAATGTGACAATAGTTT
AAACTATTGTCACATTTTGTGATTACTTACCAGGTTTCAAGGACTATAGGTGATGCATATTTAAAGAGGCGTGAATTTGCTCTTGATCCATCCATAACTC[G/A]
CTTCCGCCTTTCTGAGCCTCTTCGCCGACCTGTTCTAACAGCAGAGCCATCTATCTGCACAAGAGTTCTTTCTCTGCAAGATCAATTTGTTATTTTTGCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 1.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 98.50% | 1.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.13% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228079723 | C -> T | LOC_Os02g46080.1 | missense_variant ; p.Arg248His; MODERATE | N | Average:54.991; most accessible tissue: Callus, score: 79.824 | N | N | N | N |
| vg0228079723 | C -> T | LOC_Os02g46080.2 | missense_variant ; p.Arg248His; MODERATE | N | Average:54.991; most accessible tissue: Callus, score: 79.824 | N | N | N | N |
| vg0228079723 | C -> T | LOC_Os02g46070.1 | downstream_gene_variant ; 4421.0bp to feature; MODIFIER | N | Average:54.991; most accessible tissue: Callus, score: 79.824 | N | N | N | N |