| Variant ID: vg0424399275 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24399275 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 254. )
TCAAAATCAGGAGTGTAATTGTGCACAAATATGCTGCATCAACAAAATGCTGCCCTTACCCAAAATACAATACAAAGAAGGATATTTAAGCAGATCAGTA[T/G]
ACCACTATTACTGAATCAAGTGCAATTCTCTATTTGTAAAAAATAATAATGCAAAGTAATATTTCAGTCTAGAGCTGCTCAACAAATGGTTGAATAGCTT
AAGCTATTCAACCATTTGTTGAGCAGCTCTAGACTGAAATATTACTTTGCATTATTATTTTTTACAAATAGAGAATTGCACTTGATTCAGTAATAGTGGT[A/C]
TACTGATCTGCTTAAATATCCTTCTTTGTATTGTATTTTGGGTAAGGGCAGCATTTTGTTGATGCAGCATATTTGTGCACAATTACACTCCTGATTTTGA
| 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 | 75.20% | 24.60% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 62.60% | 37.20% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 55.80% | 44.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 73.40% | 26.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.30% | 4.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 41.70% | 57.90% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 59.20% | 40.60% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424399275 | T -> G | LOC_Os04g41130.1 | upstream_gene_variant ; 3520.0bp to feature; MODIFIER | silent_mutation | Average:48.591; most accessible tissue: Callus, score: 77.397 | N | N | N | N |
| vg0424399275 | T -> G | LOC_Os04g41150.1 | upstream_gene_variant ; 3383.0bp to feature; MODIFIER | silent_mutation | Average:48.591; most accessible tissue: Callus, score: 77.397 | N | N | N | N |
| vg0424399275 | T -> G | LOC_Os04g41140.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.591; most accessible tissue: Callus, score: 77.397 | N | N | N | N |