| Variant ID: vg1115079430 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079430 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )
ACATGATTTATTTTTTTTACTACTGCTATTGATTTCCCAGGCATAAATTCATATTATTTTTGTATACATATATAGACGTATCCCGTATCCATGTTTTTCA[G/A]
AAAATGATGTATCCTATCCATATCCGTATCCCTGTATCTCGGTAACATAGAGCAAAGGATGTTGCTTGCTGCAGATGGGGTGACGGCCGCAGCGGCAGCG
CGCTGCCGCTGCGGCCGTCACCCCATCTGCAGCAAGCAACATCCTTTGCTCTATGTTACCGAGATACAGGGATACGGATATGGATAGGATACATCATTTT[C/T]
TGAAAAACATGGATACGGGATACGTCTATATATGTATACAAAAATAATATGAATTTATGCCTGGGAAATCAATAGCAGTAGTAAAAAAAATAAATCATGT
| 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 | 86.10% | 2.80% | 9.25% | 1.78% | NA |
| All Indica | 2759 | 77.60% | 4.60% | 15.22% | 2.61% | NA |
| All Japonica | 1512 | 99.20% | 0.10% | 0.26% | 0.46% | NA |
| Aus | 269 | 94.40% | 1.90% | 2.60% | 1.12% | NA |
| Indica I | 595 | 70.40% | 3.40% | 23.19% | 3.03% | NA |
| Indica II | 465 | 81.10% | 5.20% | 13.76% | 0.00% | NA |
| Indica III | 913 | 80.40% | 5.00% | 10.95% | 3.61% | NA |
| Indica Intermediate | 786 | 77.60% | 4.70% | 15.01% | 2.67% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.26% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079430 | G -> A | LOC_Os11g26340.1 | downstream_gene_variant ; 3464.0bp to feature; MODIFIER | silent_mutation | Average:9.889; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079430 | G -> A | LOC_Os11g26360.1 | downstream_gene_variant ; 3400.0bp to feature; MODIFIER | silent_mutation | Average:9.889; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079430 | G -> A | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.889; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1115079430 | G -> DEL | N | N | silent_mutation | Average:9.889; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |