| Variant ID: vg0424399282 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24399282 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, T: 0.03, others allele: 0.00, population size: 259. )
CAGGAGTGTAATTGTGCACAAATATGCTGCATCAACAAAATGCTGCCCTTACCCAAAATACAATACAAAGAAGGATATTTAAGCAGATCAGTATACCACT[A/T]
TTACTGAATCAAGTGCAATTCTCTATTTGTAAAAAATAATAATGCAAAGTAATATTTCAGTCTAGAGCTGCTCAACAAATGGTTGAATAGCTTACAGGCA
TGCCTGTAAGCTATTCAACCATTTGTTGAGCAGCTCTAGACTGAAATATTACTTTGCATTATTATTTTTTACAAATAGAGAATTGCACTTGATTCAGTAA[T/A]
AGTGGTATACTGATCTGCTTAAATATCCTTCTTTGTATTGTATTTTGGGTAAGGGCAGCATTTTGTTGATGCAGCATATTTGTGCACAATTACACTCCTG
| 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 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 61.70% | 38.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 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 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424399282 | A -> T | LOC_Os04g41130.1 | upstream_gene_variant ; 3527.0bp to feature; MODIFIER | silent_mutation | Average:48.791; most accessible tissue: Callus, score: 77.397 | N | N | N | N |
| vg0424399282 | A -> T | LOC_Os04g41150.1 | upstream_gene_variant ; 3376.0bp to feature; MODIFIER | silent_mutation | Average:48.791; most accessible tissue: Callus, score: 77.397 | N | N | N | N |
| vg0424399282 | A -> T | LOC_Os04g41140.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.791; most accessible tissue: Callus, score: 77.397 | N | N | N | N |