| Variant ID: vg1117780036 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17780036 |
| 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: 300. )
ATACCAGCTGGACGCCCTCGACGTCTCTATTATGAGTTGCTGGATTTTGTAAGTATATCGTTCAGTTAGATTTCTTACTATACGTCTCCTTTAATTAATT[A/G]
GGTCCTTGTATATAAGTAGACTATATATAGAAAATAATATACTCCCTTTTATCGTTGTAGAATGGAGATTCAAAGGGCCCGACGGCGGAGGGTTTTCGAT
ATCGAAAACCCTCCGCCGTCGGGCCCTTTGAATCTCCATTCTACAACGATAAAAGGGAGTATATTATTTTCTATATATAGTCTACTTATATACAAGGACC[T/C]
AATTAATTAAAGGAGACGTATAGTAAGAAATCTAACTGAACGATATACTTACAAAATCCAGCAACTCATAATAGAGACGTCGAGGGCGTCCAGCTGGTAT
| 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 | 27.00% | 0.30% | 3.75% | 68.96% | NA |
| All Indica | 2759 | 10.50% | 0.50% | 4.78% | 84.20% | NA |
| All Japonica | 1512 | 55.20% | 0.00% | 1.46% | 43.39% | NA |
| Aus | 269 | 11.90% | 0.00% | 6.32% | 81.78% | NA |
| Indica I | 595 | 8.10% | 0.00% | 4.71% | 87.23% | NA |
| Indica II | 465 | 25.80% | 0.00% | 10.32% | 63.87% | NA |
| Indica III | 913 | 4.20% | 1.10% | 1.86% | 92.88% | NA |
| Indica Intermediate | 786 | 10.60% | 0.60% | 4.96% | 83.84% | NA |
| Temperate Japonica | 767 | 63.90% | 0.00% | 1.96% | 34.16% | NA |
| Tropical Japonica | 504 | 29.20% | 0.00% | 1.19% | 69.64% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 34.40% | 1.10% | 6.67% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117780036 | A -> DEL | N | N | silent_mutation | Average:6.331; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1117780036 | A -> G | LOC_Os11g30552.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.331; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |