| Variant ID: vg1126329911 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26329911 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGGAGGCCGGATCCAGTGGCGGCTGTTGGGTGGGCGTTGGAAGGCGACGCGGGCGGATCCGAGGTTTGTGGGCGTAGAAGCTGGTGGCGCCGTCGATGG[A/T]
GGCGGTCGCTCGTCGTCTTCATCGCAGCCGCCGTCAACATCGTCGTCGTCGTTGTCGCAGCTACCGCCACCATGGCCGCTCGCTCCTGCCTGCCTAAGCC
GGCTTAGGCAGGCAGGAGCGAGCGGCCATGGTGGCGGTAGCTGCGACAACGACGACGACGATGTTGACGGCGGCTGCGATGAAGACGACGAGCGACCGCC[T/A]
CCATCGACGGCGCCACCAGCTTCTACGCCCACAAACCTCGGATCCGCCCGCGTCGCCTTCCAACGCCCACCCAACAGCCGCCACTGGATCCGGCCTCCAC
| 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 | 94.30% | 5.40% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 93.40% | 6.10% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.10% | 0.43% | 0.00% | NA |
| Indica III | 913 | 94.60% | 4.30% | 1.10% | 0.00% | NA |
| Indica Intermediate | 786 | 86.60% | 13.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.10% | 10.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126329911 | A -> T | LOC_Os11g43650.1 | synonymous_variant ; p.Gly33Gly; LOW | synonymous_codon | Average:42.645; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126329911 | 3.77E-07 | 3.13E-08 | mr1133 | 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 |
| vg1126329911 | NA | 7.40E-08 | mr1133_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 |
| vg1126329911 | NA | 4.64E-07 | mr1667_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 |