| Variant ID: vg0715173240 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15173240 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 28. )
ACATGACATCGGCGCCGCCCCTCCCCCTGCTGACGTCAGCCCTGGGATGCTTTATTGCGCAATAAATACATTAAGGCTTTTCTTTAATAGTAAAAACACA[A/G]
AGAATCTTCTAAAAATCATAACTAATTCATCCGAGCTCCGTTTAAGTCCATTCAAGTCTCATTAAATTCATAAAAATGTATAGAATCCATTAAAAATGGT
ACCATTTTTAATGGATTCTATACATTTTTATGAATTTAATGAGACTTGAATGGACTTAAACGGAGCTCGGATGAATTAGTTATGATTTTTAGAAGATTCT[T/C]
TGTGTTTTTACTATTAAAGAAAAGCCTTAATGTATTTATTGCGCAATAAAGCATCCCAGGGCTGACGTCAGCAGGGGGAGGGGCGGCGCCGATGTCATGT
| 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 | 48.30% | 21.60% | 1.61% | 28.44% | NA |
| All Indica | 2759 | 21.70% | 34.10% | 1.67% | 42.59% | NA |
| All Japonica | 1512 | 96.70% | 0.20% | 0.20% | 2.91% | NA |
| Aus | 269 | 38.70% | 22.70% | 7.06% | 31.60% | NA |
| Indica I | 595 | 30.90% | 44.90% | 0.84% | 23.36% | NA |
| Indica II | 465 | 34.00% | 17.60% | 1.08% | 47.31% | NA |
| Indica III | 913 | 6.40% | 30.80% | 2.19% | 60.68% | NA |
| Indica Intermediate | 786 | 25.20% | 39.40% | 2.04% | 33.33% | NA |
| Temperate Japonica | 767 | 94.40% | 0.10% | 0.39% | 5.08% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 63.50% | 5.20% | 6.25% | 25.00% | NA |
| Intermediate | 90 | 64.40% | 15.60% | 2.22% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715173240 | A -> DEL | N | N | silent_mutation | Average:7.147; most accessible tissue: Callus, score: 20.3 | N | N | N | N |
| vg0715173240 | A -> G | LOC_Os07g26390.1 | upstream_gene_variant ; 4309.0bp to feature; MODIFIER | silent_mutation | Average:7.147; most accessible tissue: Callus, score: 20.3 | N | N | N | N |
| vg0715173240 | A -> G | LOC_Os07g26400.1 | upstream_gene_variant ; 2104.0bp to feature; MODIFIER | silent_mutation | Average:7.147; most accessible tissue: Callus, score: 20.3 | N | N | N | N |
| vg0715173240 | A -> G | LOC_Os07g26410.1 | downstream_gene_variant ; 52.0bp to feature; MODIFIER | silent_mutation | Average:7.147; most accessible tissue: Callus, score: 20.3 | N | N | N | N |
| vg0715173240 | A -> G | LOC_Os07g26400-LOC_Os07g26410 | intergenic_region ; MODIFIER | silent_mutation | Average:7.147; most accessible tissue: Callus, score: 20.3 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715173240 | NA | 1.88E-06 | mr1169 | 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 |
| vg0715173240 | 4.40E-06 | NA | mr1529 | 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 |
| vg0715173240 | 4.09E-06 | 4.07E-06 | mr1869 | 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 |