| Variant ID: vg1211683413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11683413 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGTCAACAGCGCAGCCTTCCTGTCTTTTCCAGGCTAGCGCTTACACATGTTTTATAATTGCAAAACCTAATCACAATAATCCGTAAATCTCCATGTAACA[A/G]
CATTAAACTTCGGATGATCATATCTTGGTCATACGAACCCTGAATCGACCCATTCAAGTCTCCTAATGTTTGTTATAACATAAAGAACCGTGTGCTTTCT
AGAAAGCACACGGTTCTTTATGTTATAACAAACATTAGGAGACTTGAATGGGTCGATTCAGGGTTCGTATGACCAAGATATGATCATCCGAAGTTTAATG[T/C]
TGTTACATGGAGATTTACGGATTATTGTGATTAGGTTTTGCAATTATAAAACATGTGTAAGCGCTAGCCTGGAAAAGACAGGAAGGCTGCGCTGTTGACA
| 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 | 83.10% | 0.60% | 4.87% | 11.45% | NA |
| All Indica | 2759 | 88.30% | 0.80% | 5.33% | 5.65% | NA |
| All Japonica | 1512 | 76.70% | 0.20% | 1.85% | 21.30% | NA |
| Aus | 269 | 63.20% | 0.70% | 16.73% | 19.33% | NA |
| Indica I | 595 | 98.00% | 0.20% | 0.84% | 1.01% | NA |
| Indica II | 465 | 78.90% | 1.10% | 10.11% | 9.89% | NA |
| Indica III | 913 | 86.70% | 1.20% | 5.04% | 7.01% | NA |
| Indica Intermediate | 786 | 88.20% | 0.50% | 6.23% | 5.09% | NA |
| Temperate Japonica | 767 | 94.80% | 0.10% | 0.39% | 4.69% | NA |
| Tropical Japonica | 504 | 49.60% | 0.40% | 4.17% | 45.83% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.00% | 1.66% | 22.82% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 6.25% | 4.17% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 4.44% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211683413 | A -> DEL | N | N | silent_mutation | Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg1211683413 | A -> G | LOC_Os12g20090.1 | upstream_gene_variant ; 3871.0bp to feature; MODIFIER | silent_mutation | Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg1211683413 | A -> G | LOC_Os12g20100.1 | downstream_gene_variant ; 3195.0bp to feature; MODIFIER | silent_mutation | Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg1211683413 | A -> G | LOC_Os12g20090-LOC_Os12g20100 | intergenic_region ; MODIFIER | silent_mutation | Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211683413 | 3.60E-06 | NA | mr1109 | 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 |