| Variant ID: vg0629027065 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027065 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 295. )
ACAAATTAATCGAACAAATCACTTTTACATCGTTGTATATTACAACTTATTCGGATCGTTGACAAAAACAACTTAAATTTTTGAACACACAATAATGTAC[T/G]
ACCGATTGTTTTTTCCCCAAATCCAAAAGGAAAGATTGCCATCTATCGCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATC
GATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGCGATAGATGGCAATCTTTCCTTTTGGATTTGGGGAAAAAACAATCGGT[A/C]
GTACATTATTGTGTGTTCAAAAATTTAAGTTGTTTTTGTCAACGATCCGAATAAGTTGTAATATACAACGATGTAAAAGTGATTTGTTCGATTAATTTGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.10% | 0.20% | 7.96% | 1.69% | NA |
| All Indica | 2759 | 83.50% | 0.40% | 13.27% | 2.83% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 0.00% | 3.03% | 1.18% | NA |
| Indica II | 465 | 92.00% | 0.20% | 5.81% | 1.94% | NA |
| Indica III | 913 | 74.90% | 0.50% | 22.02% | 2.52% | NA |
| Indica Intermediate | 786 | 79.10% | 0.60% | 15.27% | 4.96% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 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 | 91.10% | 0.00% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027065 | T -> G | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 158.0bp to feature; MODIFIER | silent_mutation | Average:65.176; most accessible tissue: Callus, score: 80.658 | N | N | N | N |
| vg0629027065 | T -> G | LOC_Os06g48000.1 | downstream_gene_variant ; 3573.0bp to feature; MODIFIER | silent_mutation | Average:65.176; most accessible tissue: Callus, score: 80.658 | N | N | N | N |
| vg0629027065 | T -> DEL | N | N | silent_mutation | Average:65.176; most accessible tissue: Callus, score: 80.658 | N | N | N | N |