Search for Variation information by Variation ID:
Detailed information for vg0220795440:
| Variant ID: vg0220795440 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20795440 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, T: 0.00, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
TATGCAAATTTTTGTGAGCATTACTCGTTTGTGTCTTCTCTTGAACCTCTAAGGGTGGAAGAAGCTCTTAATGATCCGGATTGGGTAATGGCGATGCAAG[A/T]
GGAGTTGAACAATTTCACCTGGAATGAAGTGTGGACTTTGGTGGAGCGACCTCGGCAAAATGTGATTGGCACAAAGTGGATCTTCCGCAACAAGCAAGAC
Reverse complement sequence
GTCTTGCTTGTTGCGGAAGATCCACTTTGTGCCAATCACATTTTGCCGAGGTCGCTCCACCAAAGTCCACACTTCATTCCAGGTGAAATTGTTCAACTCC[T/A]
CTTGCATCGCCATTACCCAATCCGGATCATTAAGAGCTTCTTCCACCCTTAGAGGTTCAAGAGAAGACACAAACGAGTAATGCTCACAAAAATTTGCATA
Allele Frequencies:
| 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 | 72.10% | 6.00% | 21.86% | 0.00% | NA |
| All Indica | 2759 | 55.00% | 9.90% | 35.16% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.53% | 0.00% | NA |
| Aus | 269 | 83.60% | 1.90% | 14.50% | 0.00% | NA |
| Indica I | 595 | 48.40% | 6.90% | 44.71% | 0.00% | NA |
| Indica II | 465 | 69.50% | 9.50% | 21.08% | 0.00% | NA |
| Indica III | 913 | 49.60% | 13.30% | 37.13% | 0.00% | NA |
| Indica Intermediate | 786 | 57.60% | 8.40% | 33.97% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.50% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 3.30% | 15.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220795440 | A -> T | LOC_Os02g34670.1 | missense_variant ; p.Glu5Val; MODERATE | nonsynonymous_codon ; E5L | Average:13.614; most accessible tissue: Callus, score: 31.6 | benign  |
1.459 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220795440 | 3.66E-06 | NA | mr1521_2 | 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 |