| Variant ID: vg0422251052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 22251052 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 123. )
AATTTATATATTTTTAAATATCCTAAATATAACAAGATTAAAAGTATAAATTGATCAAATGTGTATCGTAATATACTAATAATCTTATTTATTTTCATAT[C/T]
TGATTTCTTCGTTTATCACCAAGCTTCATTTGCCAAATGTATCACAACTATGGTAACTTCAATTTTTGGTAACTTTAAGTATTGAGGGATTAGTCCACTC
GAGTGGACTAATCCCTCAATACTTAAAGTTACCAAAAATTGAAGTTACCATAGTTGTGATACATTTGGCAAATGAAGCTTGGTGATAAACGAAGAAATCA[G/A]
ATATGAAAATAAATAAGATTATTAGTATATTACGATACACATTTGATCAATTTATACTTTTAATCTTGTTATATTTAGGATATTTAAAAATATATAAATT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.00% | 35.00% | 0.93% | 0.00% | NA |
| All Indica | 2759 | 70.40% | 28.80% | 0.76% | 0.00% | NA |
| All Japonica | 1512 | 57.50% | 41.10% | 1.32% | 0.00% | NA |
| Aus | 269 | 29.40% | 70.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 91.40% | 7.90% | 0.67% | 0.00% | NA |
| Indica II | 465 | 88.60% | 10.80% | 0.65% | 0.00% | NA |
| Indica III | 913 | 49.60% | 50.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 67.90% | 30.30% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 91.00% | 7.70% | 1.30% | 0.00% | NA |
| Tropical Japonica | 504 | 12.50% | 86.10% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 45.20% | 53.50% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 14.60% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 37.80% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0422251052 | C -> T | LOC_Os04g36859.1 | upstream_gene_variant ; 1336.0bp to feature; MODIFIER | silent_mutation | Average:47.989; most accessible tissue: Callus, score: 79.394 | N | N | N | N |
| vg0422251052 | C -> T | LOC_Os04g36859.2 | upstream_gene_variant ; 1336.0bp to feature; MODIFIER | silent_mutation | Average:47.989; most accessible tissue: Callus, score: 79.394 | N | N | N | N |
| vg0422251052 | C -> T | LOC_Os04g36850.1 | downstream_gene_variant ; 4670.0bp to feature; MODIFIER | silent_mutation | Average:47.989; most accessible tissue: Callus, score: 79.394 | N | N | N | N |
| vg0422251052 | C -> T | LOC_Os04g36859-LOC_Os04g36880 | intergenic_region ; MODIFIER | silent_mutation | Average:47.989; most accessible tissue: Callus, score: 79.394 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0422251052 | NA | 8.86E-18 | Plant_height | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0422251052 | NA | 7.87E-06 | mr1177 | 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 |
| vg0422251052 | NA | 2.12E-08 | mr1531 | Jap_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 |