Search for Variation information by Variation ID:
Detailed information for vg0205786160:
| Variant ID: vg0205786160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 5786160 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.17, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
CTCAAAAGATTGTTGAGGCTTTGGTGATGGAGTTACATTTTGGTCAAATAAAACAAATCTCTCCAAACTGAGACGAGCATGCCAAGGCAAATGAGTCAAC[G/A]
CTCCAGGTCCCATGCACCCCTGAAGTGGCGCACCAAGTTCACAGAATGTTTTTAGCATGATAATCGCATGATGCTGTGAGATCTCAGAACCACTGCCTAG
Reverse complement sequence
CTAGGCAGTGGTTCTGAGATCTCACAGCATCATGCGATTATCATGCTAAAAACATTCTGTGAACTTGGTGCGCCACTTCAGGGGTGCATGGGACCTGGAG[C/T]
GTTGACTCATTTGCCTTGGCATGCTCGTCTCAGTTTGGAGAGATTTGTTTTATTTGACCAAAATGTAACTCCATCACCAAAGCCTCAACAATCTTTTGAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.90% | 15.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 55.60% | 44.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 58.30% | 41.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 41.10% | 58.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 77.20% | 22.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 20.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0205786160 | G -> A | LOC_Os02g10900.1 | missense_variant ; p.Ala753Val; MODERATE | nonsynonymous_codon ; A753V | Average:62.656; most accessible tissue: Zhenshan97 flower, score: 75.883 | benign  |
-1.133 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0205786160 | 3.53E-07 | NA | mr1136_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 |
| vg0205786160 | 3.68E-06 | NA | mr1136_2 | Jap_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 |