| Variant ID: vg0918113380 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 18113380 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTTACCTTCTGCTTGTTGTTGCCATGAGAAATAAAAAAAAATGGCAGTTAAATTCGTGCATTGCATTGTCATGTGCAGAGAAACAGAAATCCAAGTGCA[C/T]
GAACAGAAGATAAACAAATATCAAGCTATACTTGCAGCCCGTTTGAAGGCCAAATACTTCTCTAATAAGGATTTTGATGGAGGTATTTGTGAAATCATCA
TGATGATTTCACAAATACCTCCATCAAAATCCTTATTAGAGAAGTATTTGGCCTTCAAACGGGCTGCAAGTATAGCTTGATATTTGTTTATCTTCTGTTC[G/A]
TGCACTTGGATTTCTGTTTCTCTGCACATGACAATGCAATGCACGAATTTAACTGCCATTTTTTTTTATTTCTCATGGCAACAACAAGCAGAAGGTAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0918113380 | C -> T | LOC_Os09g29800.1 | synonymous_variant ; p.His77His; LOW | N | Average:34.525; most accessible tissue: Callus, score: 55.626 | N | N | N | N |
| vg0918113380 | C -> T | LOC_Os09g29790.1 | upstream_gene_variant ; 4067.0bp to feature; MODIFIER | N | Average:34.525; most accessible tissue: Callus, score: 55.626 | N | N | N | N |
| vg0918113380 | C -> T | LOC_Os09g29810.1 | upstream_gene_variant ; 1745.0bp to feature; MODIFIER | N | Average:34.525; most accessible tissue: Callus, score: 55.626 | N | N | N | N |