| Variant ID: vg0630423181 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 30423181 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 277. )
AGTTGGATTCTTGTTTTTATCCCTCTAACAAACAATGAAAGCTTGATCTAATTCCCACTGGTTCTAGTGCAATGAAGGAAAAGAACGACAGAAAAACACA[A/T]
TTCAATTTTGTTTTTCTTCAAACATTGATTATTATAGGTTTAAAAAACATTTAGTATATCATAGATAGATTGAATGCAATTGAAACCGCGCTAAAAATTT
AAATTTTTAGCGCGGTTTCAATTGCATTCAATCTATCTATGATATACTAAATGTTTTTTAAACCTATAATAATCAATGTTTGAAGAAAAACAAAATTGAA[T/A]
TGTGTTTTTCTGTCGTTCTTTTCCTTCATTGCACTAGAACCAGTGGGAATTAGATCAAGCTTTCATTGTTTGTTAGAGGGATAAAAACAAGAATCCAACT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0630423181 | A -> T | LOC_Os06g50260.1 | upstream_gene_variant ; 1785.0bp to feature; MODIFIER | N | Average:42.911; most accessible tissue: Callus, score: 84.044 | N | N | N | N |
| vg0630423181 | A -> T | LOC_Os06g50230.1 | downstream_gene_variant ; 4336.0bp to feature; MODIFIER | N | Average:42.911; most accessible tissue: Callus, score: 84.044 | N | N | N | N |
| vg0630423181 | A -> T | LOC_Os06g50240.1 | downstream_gene_variant ; 183.0bp to feature; MODIFIER | N | Average:42.911; most accessible tissue: Callus, score: 84.044 | N | N | N | N |
| vg0630423181 | A -> T | LOC_Os06g50250.1 | intron_variant ; MODIFIER | N | Average:42.911; most accessible tissue: Callus, score: 84.044 | N | N | N | N |