| Variant ID: vg1128831356 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28831356 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.09, others allele: 0.00, population size: 209. )
TTCTGGTGCTTGTTGGCTTTGAAGAGAAACACTGAGAATCAACAAAGTATTTTTACTCGTTATAAAAACTGCCATACTGAAAGTATTTTCTCTGTCAGTA[C/T]
GGCAGTTCTCTTAACGAGTGAAAACACACTTTCTGGTGCTTGTTGGCTTTCAAGAGAAACACCAGAAGCTAATAATACGTTTAAGTACCCACATTGGAAG
CTTCCAATGTGGGTACTTAAACGTATTATTAGCTTCTGGTGTTTCTCTTGAAAGCCAACAAGCACCAGAAAGTGTGTTTTCACTCGTTAAGAGAACTGCC[G/A]
TACTGACAGAGAAAATACTTTCAGTATGGCAGTTTTTATAACGAGTAAAAATACTTTGTTGATTCTCAGTGTTTCTCTTCAAAGCCAACAAGCACCAGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.70% | 34.30% | 0.74% | 0.19% | NA |
| All Indica | 2759 | 60.40% | 38.90% | 0.36% | 0.33% | NA |
| All Japonica | 1512 | 75.90% | 23.50% | 0.53% | 0.00% | NA |
| Aus | 269 | 39.40% | 56.50% | 4.09% | 0.00% | NA |
| Indica I | 595 | 43.40% | 55.80% | 0.84% | 0.00% | NA |
| Indica II | 465 | 38.10% | 60.90% | 0.00% | 1.08% | NA |
| Indica III | 913 | 85.00% | 14.70% | 0.11% | 0.22% | NA |
| Indica Intermediate | 786 | 57.90% | 41.30% | 0.51% | 0.25% | NA |
| Temperate Japonica | 767 | 58.30% | 41.50% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 95.20% | 3.60% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 7.30% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 36.70% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128831356 | C -> T | LOC_Os11g47809.1 | downstream_gene_variant ; 2843.0bp to feature; MODIFIER | silent_mutation | Average:38.322; most accessible tissue: Callus, score: 60.557 | N | N | N | N |
| vg1128831356 | C -> T | LOC_Os11g47809-LOC_Os11g47820 | intergenic_region ; MODIFIER | silent_mutation | Average:38.322; most accessible tissue: Callus, score: 60.557 | N | N | N | N |
| vg1128831356 | C -> DEL | N | N | silent_mutation | Average:38.322; most accessible tissue: Callus, score: 60.557 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128831356 | NA | 1.32E-06 | mr1310 | 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 |
| vg1128831356 | NA | 2.20E-06 | mr1644 | 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 |
| vg1128831356 | 3.65E-06 | 3.65E-06 | mr1899 | 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 |
| vg1128831356 | NA | 4.43E-07 | mr1191_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 |
| vg1128831356 | NA | 5.29E-06 | mr1959_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 |