| Variant ID: vg0611959824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11959824 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCACACCCTGATTCCTCCCTCGAAGGATCTGGCACGGATCAGGCCTCCCATCGCTGCCTCCCTCCCACAGCGGTGGCGTCATGATCTGTGATGCACGATG[A/G]
TAATGAGGGTAAGCAGCTGAGTCCATGCAATTTTGAACTTTTTACTTTGCATCTTTGTTGTTTTACCGATTTGCTGCTGCAGTTCTGCTAATTTGCTCCT
AGGAGCAAATTAGCAGAACTGCAGCAGCAAATCGGTAAAACAACAAAGATGCAAAGTAAAAAGTTCAAAATTGCATGGACTCAGCTGCTTACCCTCATTA[T/C]
CATCGTGCATCACAGATCATGACGCCACCGCTGTGGGAGGGAGGCAGCGATGGGAGGCCTGATCCGTGCCAGATCCTTCGAGGGAGGAATCAGGGTGTGG
| 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 | 91.10% | 1.60% | 2.37% | 4.91% | NA |
| All Indica | 2759 | 92.70% | 1.30% | 2.43% | 3.59% | NA |
| All Japonica | 1512 | 87.00% | 2.60% | 2.51% | 7.87% | NA |
| Aus | 269 | 97.40% | 0.00% | 1.49% | 1.12% | NA |
| Indica I | 595 | 91.90% | 0.70% | 2.02% | 5.38% | NA |
| Indica II | 465 | 94.20% | 0.90% | 1.72% | 3.23% | NA |
| Indica III | 913 | 91.00% | 2.30% | 3.61% | 3.07% | NA |
| Indica Intermediate | 786 | 94.30% | 0.90% | 1.78% | 3.05% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.26% | 3.52% | NA |
| Tropical Japonica | 504 | 71.20% | 5.20% | 6.55% | 17.06% | NA |
| Japonica Intermediate | 241 | 91.70% | 4.60% | 1.24% | 2.49% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611959824 | A -> G | LOC_Os06g20750.1 | upstream_gene_variant ; 3373.0bp to feature; MODIFIER | silent_mutation | Average:17.231; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |
| vg0611959824 | A -> G | LOC_Os06g20750-LOC_Os06g20760 | intergenic_region ; MODIFIER | silent_mutation | Average:17.231; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |
| vg0611959824 | A -> DEL | N | N | silent_mutation | Average:17.231; most accessible tissue: Zhenshan97 flower, score: 23.247 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0611959824 | 4.39E-06 | NA | mr1607_2 | 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 |