| Variant ID: vg0228080043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28080043 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 313. )
AATAAATAACATGATCACCTTCATAATCTCTTGTAAACTACAAGAAACACAAAATCCTTCTAAAGCACAAACTTTAATTTCTATGATTTGTTGCCCTCTA[C/T]
CCCTTTACTTGGCTCCTCTAATGGGTTGTTGTGTAACAAGTGAATATGGTCCAATCATTACCAAATTAATATACAATCACAACCATCCTTGAAACCATAT
ATATGGTTTCAAGGATGGTTGTGATTGTATATTAATTTGGTAATGATTGGACCATATTCACTTGTTACACAACAACCCATTAGAGGAGCCAAGTAAAGGG[G/A]
TAGAGGGCAACAAATCATAGAAATTAAAGTTTGTGCTTTAGAAGGATTTTGTGTTTCTTGTAGTTTACAAGAGATTATGAAGGTGATCATGTTATTTATT
| 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% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.04% | 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 | 99.30% | 0.70% | 0.00% | 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 | 98.90% | 1.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228080043 | C -> T | LOC_Os02g46070.1 | downstream_gene_variant ; 4741.0bp to feature; MODIFIER | N | Average:44.852; most accessible tissue: Callus, score: 81.178 | N | N | N | N |
| vg0228080043 | C -> T | LOC_Os02g46080.1 | intron_variant ; MODIFIER | N | Average:44.852; most accessible tissue: Callus, score: 81.178 | N | N | N | N |
| vg0228080043 | C -> T | LOC_Os02g46080.2 | intron_variant ; MODIFIER | N | Average:44.852; most accessible tissue: Callus, score: 81.178 | N | N | N | N |