| Variant ID: vg0812018246 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 12018246 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, T: 0.10, others allele: 0.00, population size: 105. )
TGCTCGATGTTGGCGAAGAAGAACCCAATAGCTAATGATGACCAACGCGGACGATGAGGATGTCAATGCGTGGACGGTGGTGGGTAACGCAAATCCAGTC[A/T]
TGATTGACCGGGAAAAATATAAAAAAAAGTAAATGGCACTTTGGGTTGCAAATTCTTACCAAAGTTTCACTTTGGACCACCGTTGTAATGCTTTTTTTTT
AAAAAAAAAGCATTACAACGGTGGTCCAAAGTGAAACTTTGGTAAGAATTTGCAACCCAAAGTGCCATTTACTTTTTTTTATATTTTTCCCGGTCAATCA[T/A]
GACTGGATTTGCGTTACCCACCACCGTCCACGCATTGACATCCTCATCGTCCGCGTTGGTCATCATTAGCTATTGGGTTCTTCTTCGCCAACATCGAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 7.60% | 1.90% | 50.80% | NA |
| All Indica | 2759 | 16.30% | 9.60% | 2.79% | 71.29% | NA |
| All Japonica | 1512 | 84.70% | 5.10% | 0.26% | 9.99% | NA |
| Aus | 269 | 4.10% | 1.10% | 2.60% | 92.19% | NA |
| Indica I | 595 | 34.50% | 2.50% | 1.85% | 61.18% | NA |
| Indica II | 465 | 17.40% | 4.90% | 3.44% | 74.19% | NA |
| Indica III | 913 | 2.30% | 17.30% | 2.63% | 77.77% | NA |
| Indica Intermediate | 786 | 18.10% | 8.90% | 3.31% | 69.72% | NA |
| Temperate Japonica | 767 | 96.00% | 0.40% | 0.00% | 3.65% | NA |
| Tropical Japonica | 504 | 68.50% | 12.90% | 0.40% | 18.25% | NA |
| Japonica Intermediate | 241 | 82.60% | 3.70% | 0.83% | 12.86% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 58.90% | 6.70% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0812018246 | A -> T | LOC_Os08g20050.1 | downstream_gene_variant ; 3164.0bp to feature; MODIFIER | silent_mutation | Average:14.068; most accessible tissue: Callus, score: 79.118 | N | N | N | N |
| vg0812018246 | A -> T | LOC_Os08g20050-LOC_Os08g20060 | intergenic_region ; MODIFIER | silent_mutation | Average:14.068; most accessible tissue: Callus, score: 79.118 | N | N | N | N |
| vg0812018246 | A -> DEL | N | N | silent_mutation | Average:14.068; most accessible tissue: Callus, score: 79.118 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0812018246 | NA | 8.82E-07 | mr1733 | 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 |
| vg0812018246 | NA | 6.69E-06 | mr1749 | 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 |
| vg0812018246 | NA | 5.30E-06 | mr1816 | 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 |
| vg0812018246 | 4.27E-06 | 4.25E-06 | mr1869 | 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 |
| vg0812018246 | 3.01E-06 | 3.01E-06 | mr1869 | 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 |
| vg0812018246 | NA | 4.73E-07 | mr1886 | 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 |