| Variant ID: vg0914860628 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 14860628 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )
TTCCTATTATTTACTGTTTTACAATGGTTCCCCTTTCTTATGCTGGGAGAGCTATTCACATTAATGCTTGTCTTTCCTCCATCCCTTCTTATGCCATGGG[G/T]
TTTTATCAACTGCCTGAAGGGATTTATCAGAAATTTGACTCTATTAGAGGAAAATATTATTGGGCTAGCAATAAGCAGGGGAGAAAATACCACATTGTGA
TCACAATGTGGTATTTTCTCCCCTGCTTATTGCTAGCCCAATAATATTTTCCTCTAATAGAGTCAAATTTCTGATAAATCCCTTCAGGCAGTTGATAAAA[C/A]
CCCATGGCATAAGAAGGGATGGAGGAAAGACAAGCATTAATGTGAATAGCTCTCCCAGCATAAGAAAGGGGAACCATTGTAAAACAGTAAATAATAGGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.80% | 0.00% | 0.66% | 0.55% | NA |
| All Indica | 2759 | 98.00% | 0.00% | 1.12% | 0.87% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 97.80% | 0.00% | 0.84% | 1.34% | NA |
| Indica II | 465 | 94.20% | 0.00% | 3.66% | 2.15% | NA |
| Indica III | 913 | 98.80% | 0.00% | 0.66% | 0.55% | NA |
| Indica Intermediate | 786 | 99.50% | 0.00% | 0.38% | 0.13% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0914860628 | G -> T | LOC_Os09g24880.1 | synonymous_variant ; p.Gly2Gly; LOW | N | Average:53.185; most accessible tissue: Zhenshan97 young leaf, score: 65.804 | N | N | N | N |
| vg0914860628 | G -> T | LOC_Os09g24890.1 | upstream_gene_variant ; 4136.0bp to feature; MODIFIER | N | Average:53.185; most accessible tissue: Zhenshan97 young leaf, score: 65.804 | N | N | N | N |