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Detailed information for vg0207309711:

Variant ID: vg0207309711 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7309711
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGATGTACTATTTATCTGTGATTCATGTCATTTTTTTTAAAACCGCTAAATAGCTTAGCTGCAGCTATAGCTGGCTATAGTTGATGAAAACCATAGCC[G/A]
CTAAAGGGTTTAGCCGGAGATTTAAATCATTGACACACCTATTAAGATGCAATATCAATCCCCTCTAACCCTTTTATTAACTGAACAATCCCTAACGAAA

Reverse complement sequence

TTTCGTTAGGGATTGTTCAGTTAATAAAAGGGTTAGAGGGGATTGATATTGCATCTTAATAGGTGTGTCAATGATTTAAATCTCCGGCTAAACCCTTTAG[C/T]
GGCTATGGTTTTCATCAACTATAGCCAGCTATAGCTGCAGCTAAGCTATTTAGCGGTTTTAAAAAAAATGACATGAATCACAGATAAATAGTACATCACT

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 90.30% 9.70% 0.00% 0.00% NA
All Indica  2759 83.60% 16.40% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.20% 19.80% 0.00% 0.00% NA
Indica II  465 83.70% 16.30% 0.00% 0.00% NA
Indica III  913 83.10% 16.90% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 13.20% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 94.40% 5.60% 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
vg0207309711 G -> A LOC_Os02g13620.1 upstream_gene_variant ; 709.0bp to feature; MODIFIER silent_mutation Average:70.312; most accessible tissue: Callus, score: 89.895 N N N N
vg0207309711 G -> A LOC_Os02g13630.1 downstream_gene_variant ; 4387.0bp to feature; MODIFIER silent_mutation Average:70.312; most accessible tissue: Callus, score: 89.895 N N N N
vg0207309711 G -> A LOC_Os02g13610-LOC_Os02g13620 intergenic_region ; MODIFIER silent_mutation Average:70.312; most accessible tissue: Callus, score: 89.895 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207309711 5.26E-07 9.13E-07 mr1679 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
vg0207309711 5.29E-07 5.29E-07 mr1717 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
vg0207309711 6.70E-07 NA mr1798 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
vg0207309711 2.98E-06 7.03E-06 mr1798 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