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Detailed information for vg0208464517:

Variant ID: vg0208464517 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8464517
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, A: 0.28, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


AAATATAAAATATAATCAAGTATTTTACTATTATAATCCAAATAAATTGATTCAAAATAGTTTTAAAAAAATCAATAGGCAAGTTATATAGTCAATAAAC[T/A]
GTAAGAAGGCTTATGACATGGAAAAATTACATACACCAATATGCTTTATTGTCCGGTATATTTTACAAGACAACAAAGTTATAAGTATGTCATTTAAAAA

Reverse complement sequence

TTTTTAAATGACATACTTATAACTTTGTTGTCTTGTAAAATATACCGGACAATAAAGCATATTGGTGTATGTAATTTTTCCATGTCATAAGCCTTCTTAC[A/T]
GTTTATTGACTATATAACTTGCCTATTGATTTTTTTAAAACTATTTTGAATCAATTTATTTGGATTATAATAGTAAAATACTTGATTATATTTTATATTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.00% 16.00% 0.02% 0.00% NA
All Indica  2759 82.80% 17.20% 0.04% 0.00% NA
All Japonica  1512 83.80% 16.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 63.50% 36.30% 0.17% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 89.30% 10.70% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 15.10% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 57.70% 42.30% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0208464517 T -> A LOC_Os02g15178.1 upstream_gene_variant ; 3853.0bp to feature; MODIFIER silent_mutation Average:19.044; most accessible tissue: Callus, score: 39.88 N N N N
vg0208464517 T -> A LOC_Os02g15169.1 upstream_gene_variant ; 518.0bp to feature; MODIFIER silent_mutation Average:19.044; most accessible tissue: Callus, score: 39.88 N N N N
vg0208464517 T -> A LOC_Os02g15178-LOC_Os02g15169 intergenic_region ; MODIFIER silent_mutation Average:19.044; most accessible tissue: Callus, score: 39.88 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208464517 NA 1.19E-06 mr1277 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
vg0208464517 NA 1.92E-06 mr1336 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
vg0208464517 NA 1.69E-11 mr1410 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
vg0208464517 NA 2.16E-06 mr1174_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
vg0208464517 NA 1.36E-08 mr1277_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
vg0208464517 1.07E-07 NA mr1301_2 Jap_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
vg0208464517 NA 1.13E-07 mr1347_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