| Variant ID: vg0817358722 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17358722 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGATTCAAATACCTCATTATTCGTTTGACCGCTTGACGATGTGAAGCATGAGGAGAAGCTTGAAAGCGTGCAGACAAACACACAGCAAACTGTATGTCT[A/G]
GCCTAGAAGCAGTTAGATACAACAAAAAGATTCAATCATACTTCTATACTCCTTTTGATCAATAGCTTCACCATCTTCATCAGGATCCAACACAACTGTA
TACAGTTGTGTTGGATCCTGATGAAGATGGTGAAGCTATTGATCAAAAGGAGTATAGAAGTATGATTGAATCTTTTTGTTGTATCTAACTGCTTCTAGGC[T/C]
AGACATACAGTTTGCTGTGTGTTTGTCTGCACGCTTTCAAGCTTCTCCTCATGCTTCACATCGTCAAGCGGTCAAACGAATAATGAGGTATTTGAATCAT
| 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 | 36.00% | 6.20% | 0.95% | 56.77% | NA |
| All Indica | 2759 | 4.90% | 6.80% | 1.56% | 86.70% | NA |
| All Japonica | 1512 | 94.10% | 1.90% | 0.13% | 3.84% | NA |
| Aus | 269 | 1.10% | 27.50% | 0.00% | 71.38% | NA |
| Indica I | 595 | 8.40% | 3.00% | 0.84% | 87.73% | NA |
| Indica II | 465 | 4.30% | 5.80% | 1.94% | 87.96% | NA |
| Indica III | 913 | 2.50% | 13.10% | 1.20% | 83.13% | NA |
| Indica Intermediate | 786 | 5.50% | 2.90% | 2.29% | 89.31% | NA |
| Temperate Japonica | 767 | 95.40% | 3.70% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 90.90% | 0.20% | 0.00% | 8.93% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.83% | 2.49% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 57.80% | 4.40% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817358722 | A -> G | LOC_Os08g28450.1 | downstream_gene_variant ; 1050.0bp to feature; MODIFIER | silent_mutation | Average:8.516; most accessible tissue: Callus, score: 34.324 | N | N | N | N |
| vg0817358722 | A -> G | LOC_Os08g28430-LOC_Os08g28450 | intergenic_region ; MODIFIER | silent_mutation | Average:8.516; most accessible tissue: Callus, score: 34.324 | N | N | N | N |
| vg0817358722 | A -> DEL | N | N | silent_mutation | Average:8.516; most accessible tissue: Callus, score: 34.324 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817358722 | 5.41E-07 | 7.59E-08 | mr1040 | 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 |
| vg0817358722 | 1.04E-07 | 1.04E-07 | mr1040 | 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 |
| vg0817358722 | NA | 5.46E-08 | mr1836 | 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 |
| vg0817358722 | 1.79E-06 | 1.79E-06 | mr1852 | 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 |