Search for Variation information by Variation ID:
Detailed information for vg0819408037:
| Variant ID: vg0819408037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19408037 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTACTAGCTCTGGACTCGGGGGTCGACTTCTTCGCATGGAATTCCTCTCAGACCTGTTTCGTGATCCAAGGAAATTTCTCTCTTGGATCTAGATTCGCC[G/A]
GGTTGTAGACGAACTCGCCGACTAGCTTAGTCTTGAAGTTCTTCCAAGCATTGCCCATAACCTTGAAAGCAGCCCGCCTGAGACGGTCCTCATGCTCCGC
Reverse complement sequence
GCGGAGCATGAGGACCGTCTCAGGCGGGCTGCTTTCAAGGTTATGGGCAATGCTTGGAAGAACTTCAAGACTAAGCTAGTCGGCGAGTTCGTCTACAACC[C/T]
GGCGAATCTAGATCCAAGAGAGAAATTTCCTTGGATCACGAAACAGGTCTGAGAGGAATTCCATGCGAAGAAGTCGACCCCCGAGTCCAGAGCTAGTAGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 1.20% | 0.44% | 0.00% | NA |
| All Indica | 2759 | 97.70% | 1.60% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.30% | 1.00% | 1.68% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.10% | 0.65% | 0.00% | NA |
| Indica III | 913 | 97.70% | 2.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 1.90% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0819408037 | G -> A | LOC_Os08g31390.1 | missense_variant ; p.Pro121Leu; MODERATE | nonsynonymous_codon ; P121L | Average:20.261; most accessible tissue: Callus, score: 30.966 | probably damaging  |
2.029 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819408037 | 3.75E-07 | NA | mr1558 | 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 |