| Variant ID: vg1204022539 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4022539 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, G: 0.48, others allele: 0.00, population size: 61. )
CTCTTAGGGGCTTACCAAATTTCACTGTTAACACCTGCCCCCAAATTTTGGGCTTATCAAATTTCACTGTTAACACCTGCCCCCAAATTTTGGAGTATGA[T/G]
AACTCATCCTTCAAAATTATATTATTTTTGATCTCGATGACTCCAAAATTGGTCTTACTTTGCTTCTTCAAATCGGCTTTCATGAGCCGATGCTGTCTGC
GCAGACAGCATCGGCTCATGAAAGCCGATTTGAAGAAGCAAAGTAAGACCAATTTTGGAGTCATCGAGATCAAAAATAATATAATTTTGAAGGATGAGTT[A/C]
TCATACTCCAAAATTTGGGGGCAGGTGTTAACAGTGAAATTTGATAAGCCCAAAATTTGGGGGCAGGTGTTAACAGTGAAATTTGGTAAGCCCCTAAGAG
| 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 | 24.30% | 9.50% | 0.32% | 65.87% | NA |
| All Indica | 2759 | 2.80% | 4.40% | 0.36% | 92.46% | NA |
| All Japonica | 1512 | 62.50% | 19.20% | 0.20% | 18.06% | NA |
| Aus | 269 | 4.50% | 5.20% | 0.74% | 89.59% | NA |
| Indica I | 595 | 1.80% | 0.30% | 0.50% | 97.31% | NA |
| Indica II | 465 | 1.50% | 16.10% | 0.43% | 81.94% | NA |
| Indica III | 913 | 3.20% | 1.00% | 0.11% | 95.73% | NA |
| Indica Intermediate | 786 | 3.80% | 4.50% | 0.51% | 91.22% | NA |
| Temperate Japonica | 767 | 83.40% | 11.70% | 0.26% | 4.56% | NA |
| Tropical Japonica | 504 | 41.90% | 26.60% | 0.00% | 31.55% | NA |
| Japonica Intermediate | 241 | 39.00% | 27.80% | 0.41% | 32.78% | NA |
| VI/Aromatic | 96 | 77.10% | 8.30% | 0.00% | 14.58% | NA |
| Intermediate | 90 | 46.70% | 15.60% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204022539 | T -> DEL | N | N | silent_mutation | Average:12.226; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022539 | T -> G | LOC_Os12g07910.1 | downstream_gene_variant ; 3072.0bp to feature; MODIFIER | silent_mutation | Average:12.226; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022539 | T -> G | LOC_Os12g07920.1 | downstream_gene_variant ; 1131.0bp to feature; MODIFIER | silent_mutation | Average:12.226; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022539 | T -> G | LOC_Os12g07930.1 | downstream_gene_variant ; 145.0bp to feature; MODIFIER | silent_mutation | Average:12.226; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022539 | T -> G | LOC_Os12g07920-LOC_Os12g07930 | intergenic_region ; MODIFIER | silent_mutation | Average:12.226; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204022539 | 4.24E-06 | 4.49E-06 | mr1133_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 |
| vg1204022539 | 9.97E-07 | 5.31E-07 | mr1871_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 |
| vg1204022539 | 8.26E-06 | NA | mr1873_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 |
| vg1204022539 | 7.97E-06 | NA | mr1889_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 |