| Variant ID: vg1215879134 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15879134 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 69. )
AAAGTTGTGGCCCGTCACTGATAGGTGTCATCCATGACGGGCTTAAGTTTTATACCCATCTAACATGTCTATGCGACCATATCTCAATCGGGCACTTTTC[A/G]
GCCCGATTGAGATGACTTCCTTGTGACGGCCCACTATTTCTAAGCATATTAGAGCCCGTCACAGATAGAAGGATCTGTACTAGTGTGTAACACATACACA
TGTGTATGTGTTACACACTAGTACAGATCCTTCTATCTGTGACGGGCTCTAATATGCTTAGAAATAGTGGGCCGTCACAAGGAAGTCATCTCAATCGGGC[T/C]
GAAAAGTGCCCGATTGAGATATGGTCGCATAGACATGTTAGATGGGTATAAAACTTAAGCCCGTCATGGATGACACCTATCAGTGACGGGCCACAACTTT
| 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 | 22.20% | 5.20% | 28.78% | 43.84% | NA |
| All Indica | 2759 | 3.10% | 5.80% | 41.86% | 49.22% | NA |
| All Japonica | 1512 | 58.20% | 2.80% | 2.84% | 36.18% | NA |
| Aus | 269 | 8.20% | 12.30% | 45.72% | 33.83% | NA |
| Indica I | 595 | 0.80% | 3.50% | 30.08% | 65.55% | NA |
| Indica II | 465 | 6.70% | 8.00% | 35.70% | 49.68% | NA |
| Indica III | 913 | 0.70% | 4.30% | 53.12% | 41.95% | NA |
| Indica Intermediate | 786 | 5.50% | 8.10% | 41.35% | 45.04% | NA |
| Temperate Japonica | 767 | 88.90% | 1.80% | 1.56% | 7.69% | NA |
| Tropical Japonica | 504 | 11.90% | 0.60% | 3.97% | 83.53% | NA |
| Japonica Intermediate | 241 | 57.30% | 10.40% | 4.56% | 27.80% | NA |
| VI/Aromatic | 96 | 30.20% | 4.20% | 15.62% | 50.00% | NA |
| Intermediate | 90 | 35.60% | 6.70% | 26.67% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215879134 | A -> DEL | N | N | silent_mutation | Average:9.332; most accessible tissue: Callus, score: 24.085 | N | N | N | N |
| vg1215879134 | A -> G | LOC_Os12g27096.1 | downstream_gene_variant ; 1903.0bp to feature; MODIFIER | silent_mutation | Average:9.332; most accessible tissue: Callus, score: 24.085 | N | N | N | N |
| vg1215879134 | A -> G | LOC_Os12g27090-LOC_Os12g27096 | intergenic_region ; MODIFIER | silent_mutation | Average:9.332; most accessible tissue: Callus, score: 24.085 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215879134 | 3.71E-06 | NA | mr1692 | 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 |