| Variant ID: vg0724211178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 24211178 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 227. )
CCTCCGGGTAGAGCTAGATGCACCTGCTTTGCTCGCGCTGTGGTTACATGTGCCACGTTTCTCGTGTTCTTGATCGCTTCTCTGATCTTTCTCTCGTGTT[T/G]
TTTTTTCTCTCTTTTTTTTTCATTTCTCTTCGCGCGCGGAAACTGTTTCTTGTTACTCTTTTGATCCGGTCGCGTTTTTCTCTTTCACTTTTTATTTCTT
AAGAAATAAAAAGTGAAAGAGAAAAACGCGACCGGATCAAAAGAGTAACAAGAAACAGTTTCCGCGCGCGAAGAGAAATGAAAAAAAAAGAGAGAAAAAA[A/C]
AACACGAGAGAAAGATCAGAGAAGCGATCAAGAACACGAGAAACGTGGCACATGTAACCACAGCGCGAGCAAAGCAGGTGCATCTAGCTCTACCCGGAGG
| 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 | 77.30% | 0.50% | 12.02% | 10.11% | NA |
| All Indica | 2759 | 62.80% | 0.90% | 19.32% | 17.04% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Aus | 269 | 87.70% | 0.40% | 10.78% | 1.12% | NA |
| Indica I | 595 | 59.50% | 0.50% | 20.17% | 19.83% | NA |
| Indica II | 465 | 61.30% | 0.40% | 21.29% | 16.99% | NA |
| Indica III | 913 | 65.30% | 1.30% | 17.96% | 15.44% | NA |
| Indica Intermediate | 786 | 63.20% | 0.90% | 19.08% | 16.79% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | 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 | 91.10% | 0.00% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724211178 | T -> DEL | N | N | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211178 | T -> G | LOC_Os07g40370.1 | upstream_gene_variant ; 3213.0bp to feature; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211178 | T -> G | LOC_Os07g40390.1 | downstream_gene_variant ; 4700.0bp to feature; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |
| vg0724211178 | T -> G | LOC_Os07g40380.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.002; most accessible tissue: Callus, score: 93.754 | N | N | N | N |