| Variant ID: vg0335310039 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310039 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.05, others allele: 0.00, population size: 76. )
GTGCTTACTTTAGTACTCTCTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATTCTGACAAATCGACCTTTAATAAAAT[T/G]
TATTTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACCATTTGTCTTATTCAAAAACTTT
AAAGTTTTTGAATAAGACAAATGGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAAATA[A/C]
ATTTTATTAAAGGTCGATTTGTCAGAATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAGAGAGTACTAAAGTAAGCAC
| 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 | 75.70% | 24.20% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 63.30% | 36.60% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 60.20% | 39.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.30% | 21.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 41.50% | 58.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 68.60% | 31.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 58.80% | 41.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 22.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310039 | T -> G | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 270.0bp to feature; MODIFIER | silent_mutation | Average:62.48; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0335310039 | T -> G | LOC_Os03g62314.1 | upstream_gene_variant ; 653.0bp to feature; MODIFIER | silent_mutation | Average:62.48; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |
| vg0335310039 | T -> G | LOC_Os03g62340.1 | downstream_gene_variant ; 2412.0bp to feature; MODIFIER | silent_mutation | Average:62.48; most accessible tissue: Minghui63 root, score: 79.068 | N | N | N | N |