| Variant ID: vg0817245478 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17245478 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 241. )
AATTTCAACTAATTGATAGTCTTTAAATGTTTGCTGAACCAAGGTTTTAAGGTAGATGGCATTGCAAAATGTTTGTAATAATTGTTTTGATAAAAAGTTA[A/G]
TGAGCTGCAAGTTCTTACCACTGCATCTGACCACCTGACATAAAGCTAGCTGAATATGACCATGATCCATCTGTAGCTTTGCACATTAGGCCTTGTTTAG
CTAAACAAGGCCTAATGTGCAAAGCTACAGATGGATCATGGTCATATTCAGCTAGCTTTATGTCAGGTGGTCAGATGCAGTGGTAAGAACTTGCAGCTCA[T/C]
TAACTTTTTATCAAAACAATTATTACAAACATTTTGCAATGCCATCTACCTTAAAACCTTGGTTCAGCAAACATTTAAAGACTATCAATTAGTTGAAATT
| 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 | 86.80% | 2.30% | 1.69% | 9.18% | NA |
| All Indica | 2759 | 83.30% | 0.00% | 1.09% | 15.59% | NA |
| All Japonica | 1512 | 89.40% | 7.20% | 3.24% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 70.10% | 0.00% | 2.52% | 27.39% | NA |
| Indica II | 465 | 98.10% | 0.00% | 0.22% | 1.72% | NA |
| Indica III | 913 | 81.50% | 0.00% | 0.44% | 18.07% | NA |
| Indica Intermediate | 786 | 86.80% | 0.00% | 1.27% | 11.96% | NA |
| Temperate Japonica | 767 | 88.00% | 8.00% | 4.04% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 1.40% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 76.80% | 17.00% | 6.22% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817245478 | A -> G | LOC_Os08g28260.1 | upstream_gene_variant ; 1751.0bp to feature; MODIFIER | silent_mutation | Average:32.699; most accessible tissue: Callus, score: 68.272 | N | N | N | N |
| vg0817245478 | A -> G | LOC_Os08g28250.1 | downstream_gene_variant ; 4245.0bp to feature; MODIFIER | silent_mutation | Average:32.699; most accessible tissue: Callus, score: 68.272 | N | N | N | N |
| vg0817245478 | A -> G | LOC_Os08g28250-LOC_Os08g28260 | intergenic_region ; MODIFIER | silent_mutation | Average:32.699; most accessible tissue: Callus, score: 68.272 | N | N | N | N |
| vg0817245478 | A -> DEL | N | N | silent_mutation | Average:32.699; most accessible tissue: Callus, score: 68.272 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817245478 | 4.06E-06 | 4.06E-06 | mr1015 | Jap_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 |
| vg0817245478 | 1.64E-06 | 1.64E-06 | mr1806 | Jap_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 |
| vg0817245478 | NA | 4.57E-06 | mr1903 | Jap_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 |