| Variant ID: vg0409852831 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9852831 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 128. )
GACATGAGGAGGGATCAACATGACCATTATGAGGTAAGTGATGATGTTCTAGGTAAGATCAAATCTGCACTGCCTTATTTCGAGGGAAACTATGATCCTC[G/A]
TGCTTACATTAATTGGGAGCTAGCGGTTGATAGTGAATTTCAAAAGCATGTCTTGTCAGAGAAACAAAAGGTTATGTGTGCCTCTAGTGTTTTAATTAAA
TTTAATTAAAACACTAGAGGCACACATAACCTTTTGTTTCTCTGACAAGACATGCTTTTGAAATTCACTATCAACCGCTAGCTCCCAATTAATGTAAGCA[C/T]
GAGGATCATAGTTTCCCTCGAAATAAGGCAGTGCAGATTTGATCTTACCTAGAACATCATCACTTACCTCATAATGGTCATGTTGATCCCTCCTCATGTC
| 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 | 0.10% | 0.10% | 0.80% | 98.96% | NA |
| All Indica | 2759 | 0.30% | 0.10% | 1.34% | 98.30% | NA |
| All Japonica | 1512 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Aus | 269 | 0.00% | 0.40% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.20% | 0.34% | 99.50% | NA |
| Indica II | 465 | 0.40% | 0.20% | 1.29% | 98.06% | NA |
| Indica III | 913 | 0.30% | 0.10% | 2.19% | 97.37% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 1.15% | 98.60% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 1.11% | 98.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409852831 | G -> A | LOC_Os04g17920.1 | missense_variant ; p.Arg54His; MODERATE | N | Average:11.231; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0409852831 | G -> A | LOC_Os04g17910.1 | upstream_gene_variant ; 2136.0bp to feature; MODIFIER | N | Average:11.231; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0409852831 | G -> A | LOC_Os04g17900.1 | downstream_gene_variant ; 4457.0bp to feature; MODIFIER | N | Average:11.231; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0409852831 | G -> A | LOC_Os04g17930.1 | downstream_gene_variant ; 3306.0bp to feature; MODIFIER | N | Average:11.231; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |