| Variant ID: vg1121128751 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21128751 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.29, others allele: 0.00, population size: 55. )
CACAGGTAAATACTCACCTGTGACGGGTATATATAAGGACCCGACACATAATGATTGTGACGTGTCCACATATAAACCCGTCACTGATGAGTACTTACCT[A/G]
TGACGGGTTTTAAGTTTACACCCGTCAAAGATGAGTAACCTCACCTCATATATTCAATTAATTTTCACTTATAAAAAAGGAAACACCAACCCTCCCCTAC
GTAGGGGAGGGTTGGTGTTTCCTTTTTTATAAGTGAAAATTAATTGAATATATGAGGTGAGGTTACTCATCTTTGACGGGTGTAAACTTAAAACCCGTCA[T/C]
AGGTAAGTACTCATCAGTGACGGGTTTATATGTGGACACGTCACAATCATTATGTGTCGGGTCCTTATATATACCCGTCACAGGTGAGTATTTACCTGTG
| 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 | 52.60% | 33.90% | 11.93% | 1.59% | NA |
| All Indica | 2759 | 33.10% | 48.70% | 16.93% | 1.27% | NA |
| All Japonica | 1512 | 90.10% | 4.00% | 3.90% | 2.05% | NA |
| Aus | 269 | 26.00% | 63.60% | 9.67% | 0.74% | NA |
| Indica I | 595 | 32.10% | 48.20% | 19.50% | 0.17% | NA |
| Indica II | 465 | 15.50% | 51.80% | 31.83% | 0.86% | NA |
| Indica III | 913 | 43.00% | 47.60% | 7.89% | 1.42% | NA |
| Indica Intermediate | 786 | 32.70% | 48.50% | 16.67% | 2.16% | NA |
| Temperate Japonica | 767 | 95.00% | 3.50% | 0.78% | 0.65% | NA |
| Tropical Japonica | 504 | 80.80% | 4.80% | 9.52% | 4.96% | NA |
| Japonica Intermediate | 241 | 93.80% | 3.70% | 2.07% | 0.41% | NA |
| VI/Aromatic | 96 | 91.70% | 3.10% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 57.80% | 26.70% | 10.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121128751 | A -> DEL | N | N | silent_mutation | Average:62.597; most accessible tissue: Zhenshan97 young leaf, score: 86.698 | N | N | N | N |
| vg1121128751 | A -> G | LOC_Os11g35960.1 | upstream_gene_variant ; 2918.0bp to feature; MODIFIER | silent_mutation | Average:62.597; most accessible tissue: Zhenshan97 young leaf, score: 86.698 | N | N | N | N |
| vg1121128751 | A -> G | LOC_Os11g35950-LOC_Os11g35960 | intergenic_region ; MODIFIER | silent_mutation | Average:62.597; most accessible tissue: Zhenshan97 young leaf, score: 86.698 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121128751 | NA | 4.17E-08 | mr1580_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 |
| vg1121128751 | NA | 1.55E-06 | mr1807_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 |
| vg1121128751 | NA | 1.21E-07 | mr1825_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 |
| vg1121128751 | NA | 8.00E-06 | mr1882_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 |