| Variant ID: vg1225600237 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600237 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )
TAGCAATTCTCTTGTTCTTGCGAAGCAACAAGCTAGGATCATAAGGTGTTGGAGAAGGCTTACTATCAATATAGCCAAAACGATTCAAGATCTTCTCCAC[A/G]
TAATGGGACTGCAAGAGTGTAATCCCATTCTCACCTCTAATTAGCTTAATGTTTAAGATAACATCAGCTACTCCCAAATCCTTCATATCAAAATTTTGAG
CTCAAAATTTTGATATGAAGGATTTGGGAGTAGCTGATGTTATCTTAAACATTAAGCTAATTAGAGGTGAGAATGGGATTACACTCTTGCAGTCCCATTA[T/C]
GTGGAGAAGATCTTGAATCGTTTTGGCTATATTGATAGTAAGCCTTCTCCAACACCTTATGATCCTAGCTTGTTGCTTCGCAAGAACAAGAGAATTGCTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.40% | 0.10% | 8.57% | 30.94% | NA |
| All Indica | 2759 | 43.70% | 0.10% | 13.63% | 42.55% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 2.60% | 0.00% | 7.06% | 90.33% | NA |
| Indica I | 595 | 87.10% | 0.00% | 3.03% | 9.92% | NA |
| Indica II | 465 | 19.80% | 0.00% | 14.41% | 65.81% | NA |
| Indica III | 913 | 31.00% | 0.20% | 22.12% | 46.66% | NA |
| Indica Intermediate | 786 | 39.90% | 0.00% | 11.32% | 48.73% | 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 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 69.80% | 3.10% | 2.08% | 25.00% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 8.89% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600237 | A -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:14.493; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg1225600237 | A -> G | LOC_Os12g41280.1 | synonymous_variant ; p.Tyr1042Tyr; LOW | synonymous_codon | Average:14.493; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |