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Detailed information for vg0316680679:

Variant ID: vg0316680679 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16680679
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TTAAACATAAATCTCCATTTAACATAAGTCCCAATTTAACAATCCACAATTAAACATTCTCAAAATTAAACAATCCACAATTGCACATATCACAATCCAC[G/A]
ATCCACAATTAAACAATCCACAATCCACAATTGCACATTTCACATTTCTTTTTTTTTAAAGTAAATGTTACCGGGGGACTTTGGACCGGAGGAGGTATTG

Reverse complement sequence

CAATACCTCCTCCGGTCCAAAGTCCCCCGGTAACATTTACTTTAAAAAAAAAGAAATGTGAAATGTGCAATTGTGGATTGTGGATTGTTTAATTGTGGAT[C/T]
GTGGATTGTGATATGTGCAATTGTGGATTGTTTAATTTTGAGAATGTTTAATTGTGGATTGTTAAATTGGGACTTATGTTAAATGGAGATTTATGTTTAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.20% 11.60% 0.19% 0.00% NA
All Indica  2759 84.80% 14.90% 0.29% 0.00% NA
All Japonica  1512 92.30% 7.70% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 63.40% 36.10% 0.50% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 93.60% 6.20% 0.11% 0.00% NA
Indica Intermediate  786 84.50% 15.00% 0.51% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 77.80% 22.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0316680679 G -> A LOC_Os03g29290.1 upstream_gene_variant ; 738.0bp to feature; MODIFIER silent_mutation Average:47.009; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N
vg0316680679 G -> A LOC_Os03g29310.1 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:47.009; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N
vg0316680679 G -> A LOC_Os03g29290-LOC_Os03g29310 intergenic_region ; MODIFIER silent_mutation Average:47.009; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316680679 NA 8.56E-06 mr1038 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
vg0316680679 NA 3.40E-06 mr1038 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
vg0316680679 6.45E-06 6.45E-06 mr1398 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
vg0316680679 NA 3.52E-06 mr1542 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
vg0316680679 3.97E-06 1.75E-06 mr1545 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
vg0316680679 1.13E-08 1.13E-08 mr1545 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
vg0316680679 4.83E-08 4.83E-08 mr1674 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