| Variant ID: vg0526335924 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 26335924 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 281. )
GAAGGTGCTGCTTTGACAGATGAATAGGCAAAAGAAGTGTAGAGTCACGAACAAATAATAAAGGTCCCAGCTGAACAAGGAAAAGCGGAGCATTTTCATC[G/T]
CCAGAATTTGAACCACCACGCGACGACTCCAACCTCCAAAGGTCCCCACGTGCAACAACTGAAGTCTCAAAGTCATGGTGCCTGGTCTCGTATGTTGCTG
CAGCAACATACGAGACCAGGCACCATGACTTTGAGACTTCAGTTGTTGCACGTGGGGACCTTTGGAGGTTGGAGTCGTCGCGTGGTGGTTCAAATTCTGG[C/A]
GATGAAAATGCTCCGCTTTTCCTTGTTCAGCTGGGACCTTTATTATTTGTTCGTGACTCTACACTTCTTTTGCCTATTCATCTGTCAAAGCAGCACCTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0526335924 | G -> T | LOC_Os05g45400.1 | synonymous_variant ; p.Gly259Gly; LOW | N | Average:53.632; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 | N | N | N | N |
| vg0526335924 | G -> T | LOC_Os05g45390.1 | upstream_gene_variant ; 4586.0bp to feature; MODIFIER | N | Average:53.632; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 | N | N | N | N |