| Variant ID: vg0234311127 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34311127 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )
AATTCTATTCGAGAATCTCCATCCGAAATTTTCTTCATGTTGGTACAATTAGAATTGAGATGCAGAAATTTCTCACAATTTGATCCACATGCCTTTTCAT[A/G]
GGGTGTTTTTTTGCTACGTAGAGAAGATAATTACTTACGAATTCCAAGAATACCATTATCGGAACAACTCTGCGATGTTGGCGACGATGGTGGGTTTGGA
TCCAAACCCACCATCGTCGCCAACATCGCAGAGTTGTTCCGATAATGGTATTCTTGGAATTCGTAAGTAATTATCTTCTCTACGTAGCAAAAAAACACCC[T/C]
ATGAAAAGGCATGTGGATCAAATTGTGAGAAATTTCTGCATCTCAATTCTAATTGTACCAACATGAAGAAAATTTCGGATGGAGATTCTCGAATAGAATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.60% | 17.10% | 0.23% | 0.08% | NA |
| All Indica | 2759 | 73.30% | 26.20% | 0.36% | 0.14% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 76.20% | 23.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 56.50% | 42.90% | 0.67% | 0.00% | NA |
| Indica II | 465 | 87.70% | 11.80% | 0.43% | 0.00% | NA |
| Indica III | 913 | 80.40% | 19.40% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 69.10% | 30.20% | 0.51% | 0.25% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 6.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234311127 | A -> G | LOC_Os02g56040.1 | upstream_gene_variant ; 3398.0bp to feature; MODIFIER | silent_mutation | Average:33.793; most accessible tissue: Callus, score: 47.253 | N | N | N | N |
| vg0234311127 | A -> G | LOC_Os02g56060.1 | upstream_gene_variant ; 1579.0bp to feature; MODIFIER | silent_mutation | Average:33.793; most accessible tissue: Callus, score: 47.253 | N | N | N | N |
| vg0234311127 | A -> G | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.793; most accessible tissue: Callus, score: 47.253 | N | N | N | N |
| vg0234311127 | A -> DEL | N | N | silent_mutation | Average:33.793; most accessible tissue: Callus, score: 47.253 | N | N | N | N |