| Variant ID: vg1119943497 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19943497 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.65, A: 0.35, others allele: 0.00, population size: 84. )
AGCGTGAAAAAAATATCAAACAAATAAAACAAAAATAAAAAATTTCGGGGGGGAGGGGCGCCAGCCACTCTGGCGCACTCCCCCTAGCCACCTCAGCATC[A/G]
CCCCGCCACGTCGGCAGGGGGACGGCGCCAAAGAGGCTGGCGCCGTCCTGTTGAACGACGGCGCCAGCCACTCTGGCGCCCTAAAAAGGACTATTTTTGG
CCAAAAATAGTCCTTTTTAGGGCGCCAGAGTGGCTGGCGCCGTCGTTCAACAGGACGGCGCCAGCCTCTTTGGCGCCGTCCCCCTGCCGACGTGGCGGGG[T/C]
GATGCTGAGGTGGCTAGGGGGAGTGCGCCAGAGTGGCTGGCGCCCCTCCCCCCCGAAATTTTTTATTTTTGTTTTATTTGTTTGATATTTTTTTCACGCT
| 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 | 77.10% | 22.20% | 0.72% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 1.40% | 1.01% | 0.00% | NA |
| All Japonica | 1512 | 39.20% | 60.60% | 0.20% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 96.70% | 0.80% | 2.52% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 2.80% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 19.60% | 80.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 53.80% | 46.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 71.00% | 28.20% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 30.20% | 67.70% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 31.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119943497 | A -> G | LOC_Os11g34080.1 | downstream_gene_variant ; 2868.0bp to feature; MODIFIER | silent_mutation | Average:70.555; most accessible tissue: Zhenshan97 flower, score: 90.278 | N | N | N | N |
| vg1119943497 | A -> G | LOC_Os11g34080-LOC_Os11g34090 | intergenic_region ; MODIFIER | silent_mutation | Average:70.555; most accessible tissue: Zhenshan97 flower, score: 90.278 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119943497 | 4.73E-06 | 2.25E-06 | mr1838 | 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 |
| vg1119943497 | NA | 5.68E-09 | mr1624_2 | 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 |
| vg1119943497 | NA | 7.24E-09 | mr1741_2 | 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 |