Search for Variation information by Variation ID:
Detailed information for vg0136012413:
| Variant ID: vg0136012413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36012413 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.11, T: 0.00, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
GGCAGTTTGGATGACAGCGTCCTGGCGTTCAAAAAGATCAAGAACAAGAACGTGGTGTCCTGGAACGCGTTGATCTGCGGATATGCGCAAAATGGGAGGG[G/T]
GGAGGAGGCTTTGGATGCCTTCAGGAGGATGAAAGCTACAGGCTTGAAGCTGGATCGTGTTACTCTTCTTGGCTTGCTGTTTGGTTGCAACCATGCTGGT
Reverse complement sequence
ACCAGCATGGTTGCAACCAAACAGCAAGCCAAGAAGAGTAACACGATCCAGCTTCAAGCCTGTAGCTTTCATCCTCCTGAAGGCATCCAAAGCCTCCTCC[C/A]
CCCTCCCATTTTGCGCATATCCGCAGATCAACGCGTTCCAGGACACCACGTTCTTGTTCTTGATCTTTTTGAACGCCAGGACGCTGTCATCCAAACTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 61.20% | 38.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 74.20% | 25.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136012413 | G -> T | LOC_Os01g62220.1 | missense_variant ; p.Gly255Val; MODERATE | nonsynonymous_codon ; G255V | Average:72.981; most accessible tissue: Zhenshan97 panicle, score: 84.824 | probably damaging  |
2.519 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136012413 | NA | 1.10E-07 | mr1213 | 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 |
| vg0136012413 | NA | 6.95E-06 | mr1887 | 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 |
| vg0136012413 | NA | 1.58E-06 | mr1887 | 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 |