| Variant ID: vg1116975625 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16975625 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, T: 0.33, others allele: 0.00, population size: 195. )
TTTATAAAATTCATCATCTTTGGGTTCAGAGTACACATGTTTGCACGTTCTCTCGTGGAGATGTTGAAATGAACCTCAAATAATTGAGAATGTCCCACAT[T/G]
TTCCCTTGAAGTTGAAGAAGCTGATGTTTTTAGCTCAGCTTGACAAGGCTTGAAAAGATCCCTGTTTGACTTACTATAGCTAGCTATAATAACAAATTAC
GTAATTTGTTATTATAGCTAGCTATAGTAAGTCAAACAGGGATCTTTTCAAGCCTTGTCAAGCTGAGCTAAAAACATCAGCTTCTTCAACTTCAAGGGAA[A/C]
ATGTGGGACATTCTCAATTATTTGAGGTTCATTTCAACATCTCCACGAGAGAACGTGCAAACATGTGTACTCTGAACCCAAAGATGATGAATTTTATAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 2.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1116975625 | T -> G | LOC_Os11g29274.1 | downstream_gene_variant ; 349.0bp to feature; MODIFIER | silent_mutation | Average:41.832; most accessible tissue: Zhenshan97 flower, score: 66.841 | N | N | N | N |
| vg1116975625 | T -> G | LOC_Os11g29274-LOC_Os11g29290 | intergenic_region ; MODIFIER | silent_mutation | Average:41.832; most accessible tissue: Zhenshan97 flower, score: 66.841 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116975625 | NA | 7.39E-06 | mr1740 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1116975625 | NA | 4.50E-06 | mr1236_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1116975625 | 1.23E-06 | 7.14E-10 | mr1959_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |