| Variant ID: vg1115079678 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079678 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 112. )
AGAGCAGGCAGGGCGAGCATTGCTAGCGTAGAATAGCTCAGATGAGTTATGTTTGTTTCTGAATTTCTGTCTTTGTTTCTGAATTTCTGTCTCCCACAAG[G/A]
TTACCTTGGTTATACTGCACAATATCCAAATTTGCTATACACGGTCTCTCATATTTATTAATTTCTTCAGTTTGTCCAATTTCCCATATGAATTTTGAAA
TTTCAAAATTCATATGGGAAATTGGACAAACTGAAGAAATTAATAAATATGAGAGACCGTGTATAGCAAATTTGGATATTGTGCAGTATAACCAAGGTAA[C/T]
CTTGTGGGAGACAGAAATTCAGAAACAAAGACAGAAATTCAGAAACAAACATAACTCATCTGAGCTATTCTACGCTAGCAATGCTCGCCCTGCCTGCTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.00% | 3.30% | 13.69% | 0.00% | NA |
| All Indica | 2759 | 72.40% | 5.30% | 22.25% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 0.20% | 1.06% | 0.00% | NA |
| Aus | 269 | 96.30% | 1.10% | 2.60% | 0.00% | NA |
| Indica I | 595 | 68.70% | 2.40% | 28.91% | 0.00% | NA |
| Indica II | 465 | 77.60% | 4.50% | 17.85% | 0.00% | NA |
| Indica III | 913 | 71.50% | 6.60% | 21.91% | 0.00% | NA |
| Indica Intermediate | 786 | 73.20% | 6.60% | 20.23% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.10% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.20% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 3.30% | 11.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079678 | G -> A | LOC_Os11g26340.1 | downstream_gene_variant ; 3712.0bp to feature; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079678 | G -> A | LOC_Os11g26360.1 | downstream_gene_variant ; 3152.0bp to feature; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |
| vg1115079678 | G -> A | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |