| Variant ID: vg1121167517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21167517 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.37, others allele: 0.00, population size: 54. )
TATTTCTTGCTTGTTGTCTAGTGTCCGTGCCATCTCAAGATCTCAAATCCCCGATCTATCGTCGAGTTCAATCCCGAATCCAAATCCTTCCAAATCAATT[T/C]
CTCCGCAAAAGTCTATTTTGCCTCCCCCAGGGTCGATGGGCCAAATTTCTCTCGGCCCATCTCCCCCCTTCCTCCCGGCTATCTCTCTCTCTCTCTCCCT
AGGGAGAGAGAGAGAGAGATAGCCGGGAGGAAGGGGGGAGATGGGCCGAGAGAAATTTGGCCCATCGACCCTGGGGGAGGCAAAATAGACTTTTGCGGAG[A/G]
AATTGATTTGGAAGGATTTGGATTCGGGATTGAACTCGACGATAGATCGGGGATTTGAGATCTTGAGATGGCACGGACACTAGACAACAAGCAAGAAATA
| 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 | 27.70% | 23.10% | 0.66% | 48.54% | NA |
| All Indica | 2759 | 24.90% | 7.70% | 0.83% | 66.58% | NA |
| All Japonica | 1512 | 35.80% | 54.50% | 0.26% | 9.46% | NA |
| Aus | 269 | 21.20% | 12.60% | 0.74% | 65.43% | NA |
| Indica I | 595 | 37.30% | 21.80% | 0.84% | 40.00% | NA |
| Indica II | 465 | 4.90% | 3.90% | 1.29% | 89.89% | NA |
| Indica III | 913 | 30.30% | 1.00% | 0.44% | 68.24% | NA |
| Indica Intermediate | 786 | 20.90% | 7.10% | 1.02% | 70.99% | NA |
| Temperate Japonica | 767 | 13.40% | 80.10% | 0.39% | 6.13% | NA |
| Tropical Japonica | 504 | 72.20% | 10.90% | 0.20% | 16.67% | NA |
| Japonica Intermediate | 241 | 30.70% | 64.30% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 1.04% | 91.67% | NA |
| Intermediate | 90 | 21.10% | 22.20% | 1.11% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121167517 | T -> DEL | N | N | silent_mutation | Average:22.096; most accessible tissue: Callus, score: 77.66 | N | N | N | N |
| vg1121167517 | T -> C | LOC_Os11g36010.1 | downstream_gene_variant ; 1922.0bp to feature; MODIFIER | silent_mutation | Average:22.096; most accessible tissue: Callus, score: 77.66 | N | N | N | N |
| vg1121167517 | T -> C | LOC_Os11g36010-LOC_Os11g36020 | intergenic_region ; MODIFIER | silent_mutation | Average:22.096; most accessible tissue: Callus, score: 77.66 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121167517 | 2.66E-06 | 2.66E-06 | mr1329 | 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 |
| vg1121167517 | 8.40E-06 | 8.40E-06 | mr1524 | 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 |
| vg1121167517 | NA | 9.64E-12 | mr1540 | 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 |
| vg1121167517 | 4.75E-06 | 1.87E-07 | mr1745 | 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 |