| Variant ID: vg1118908807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18908807 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGGATCCTAATTTGAGAGGAAGGCCACGTTCTAAACTAACTGACTTGTTTCCCGTTAGCAGTTAGCACGTTTTCCAAACTGTTAAATACTATATAAGAC[T/G]
GCTAACTGTTCGTTTTTTTTAAAAAAAATACATATAAAAGTTTTTAAAAAACAAACAAATCATTTTTCTAAAATTTATAATAATAGTTATTAATATTTAA
TTAAATATTAATAACTATTATTATAAATTTTAGAAAAATGATTTGTTTGTTTTTTAAAAACTTTTATATGTATTTTTTTTAAAAAAAACGAACAGTTAGC[A/C]
GTCTTATATAGTATTTAACAGTTTGGAAAACGTGCTAACTGCTAACGGGAAACAAGTCAGTTAGTTTAGAACGTGGCCTTCCTCTCAAATTAGGATCCAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.50% | 11.40% | 3.15% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.40% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 59.10% | 31.80% | 9.06% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.60% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 72.50% | 15.50% | 11.99% | 0.00% | NA |
| Tropical Japonica | 504 | 40.10% | 54.80% | 5.16% | 0.00% | NA |
| Japonica Intermediate | 241 | 56.40% | 35.70% | 7.88% | 0.00% | NA |
| VI/Aromatic | 96 | 60.40% | 35.40% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1118908807 | T -> G | LOC_Os11g32090.1 | upstream_gene_variant ; 4260.0bp to feature; MODIFIER | silent_mutation | Average:40.327; most accessible tissue: Callus, score: 65.502 | N | N | N | N |
| vg1118908807 | T -> G | LOC_Os11g32090-LOC_Os11g32100 | intergenic_region ; MODIFIER | silent_mutation | Average:40.327; most accessible tissue: Callus, score: 65.502 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118908807 | 4.77E-06 | NA | mr1141 | 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 |
| vg1118908807 | 9.50E-06 | NA | mr1241 | 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 |
| vg1118908807 | NA | 1.54E-06 | mr1404 | 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 |