| Variant ID: vg0220098143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20098143 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 103. )
ACCAACGCGCCTATTAGCGGATCACCGGATCCGTTCCCTGTCCCTCCCACAGCAGTAGAGGCGTGAGATGATGTAGAACACCCACGCCCATCCCTTTGCA[C/T]
TCAAGAACATTGCAGAAGTAGACAATAAACATAGATATAGGGTGGAGCTATCTCTTCATTATAGATCTCATCTGAAGTACAAGCCAGCCATCAGCTATAG
CTATAGCTGATGGCTGGCTTGTACTTCAGATGAGATCTATAATGAAGAGATAGCTCCACCCTATATCTATGTTTATTGTCTACTTCTGCAATGTTCTTGA[G/A]
TGCAAAGGGATGGGCGTGGGTGTTCTACATCATCTCACGCCTCTACTGCTGTGGGAGGGACAGGGAACGGATCCGGTGATCCGCTAATAGGCGCGTTGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.30% | 32.20% | 2.43% | 0.00% | NA |
| All Indica | 2759 | 89.60% | 9.40% | 1.01% | 0.00% | NA |
| All Japonica | 1512 | 26.20% | 68.40% | 5.42% | 0.00% | NA |
| Aus | 269 | 66.50% | 33.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 85.40% | 12.30% | 2.35% | 0.00% | NA |
| Indica II | 465 | 79.80% | 19.80% | 0.43% | 0.00% | NA |
| Indica III | 913 | 96.30% | 3.40% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 91.00% | 7.90% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 42.00% | 50.20% | 7.82% | 0.00% | NA |
| Tropical Japonica | 504 | 7.90% | 89.90% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 14.10% | 81.30% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 55.60% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0220098143 | C -> T | LOC_Os02g33700.1 | upstream_gene_variant ; 4625.0bp to feature; MODIFIER | silent_mutation | Average:64.292; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0220098143 | C -> T | LOC_Os02g33690-LOC_Os02g33700 | intergenic_region ; MODIFIER | silent_mutation | Average:64.292; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220098143 | NA | 2.52E-10 | mr1379_2 | 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 |
| vg0220098143 | NA | 2.28E-08 | mr1559_2 | 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 |
| vg0220098143 | NA | 8.79E-07 | mr1627_2 | 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 |
| vg0220098143 | 3.82E-06 | 8.95E-08 | mr1977_2 | 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 |
| vg0220098143 | NA | 1.59E-08 | mr1993_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 |