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Detailed information for vg0232306661:

Variant ID: vg0232306661 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32306661
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTAGGAAAGTGTGTTTAGTGTCCGATAAGGACTTTATATTTTCCTTTTATCTTTAGGTTAGTTTCTTTCTTGTCTGACAAGGACTTGTATCAACCCAT[G/A]
GGTATAAATATGTACACCCGGGGTCTATGTAATATATCCTCACGATCAATACAATTCGGCGCATCGCCACCTTTTACCTTTTCTACTTTATTTTATCGTC

Reverse complement sequence

GACGATAAAATAAAGTAGAAAAGGTAAAAGGTGGCGATGCGCCGAATTGTATTGATCGTGAGGATATATTACATAGACCCCGGGTGTACATATTTATACC[C/T]
ATGGGTTGATACAAGTCCTTGTCAGACAAGAAAGAAACTAACCTAAAGATAAAAGGAAAATATAAAGTCCTTATCGGACACTAAACACACTTTCCTAAAG

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 93.30% 6.00% 0.70% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 80.40% 17.50% 2.12% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 66.10% 30.00% 3.91% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 86.30% 13.30% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 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
vg0232306661 G -> A LOC_Os02g52830.1 upstream_gene_variant ; 2679.0bp to feature; MODIFIER silent_mutation Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0232306661 G -> A LOC_Os02g52840.1 downstream_gene_variant ; 4138.0bp to feature; MODIFIER silent_mutation Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0232306661 G -> A LOC_Os02g52830-LOC_Os02g52840 intergenic_region ; MODIFIER silent_mutation Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232306661 5.97E-07 NA mr1486 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
vg0232306661 6.51E-06 3.74E-11 mr1486 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