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Detailed information for vg0431034778:

Variant ID: vg0431034778 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31034778
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGATAAAATTTCGAAAGAAAATTTGTGTAAATATTAACATCCGTAGAAGGACTGGTTGCATTTGGGATTTTCTTTCGGATCGATACGAGGACAATGCC[G/A]
CTAATAAATACCTAATATATATAAGTTGCATATATAATTGCATTGTTTGAACCATGTTCCACATAAATATTTCAACGATTTATATCACATATCTTCCAAA

Reverse complement sequence

TTTGGAAGATATGTGATATAAATCGTTGAAATATTTATGTGGAACATGGTTCAAACAATGCAATTATATATGCAACTTATATATATTAGGTATTTATTAG[C/T]
GGCATTGTCCTCGTATCGATCCGAAAGAAAATCCCAAATGCAACCAGTCCTTCTACGGATGTTAATATTTACACAAATTTTCTTTCGAAATTTTATCTCG

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 83.00% 16.70% 0.30% 0.00% NA
All Indica  2759 86.70% 12.80% 0.43% 0.00% NA
All Japonica  1512 81.00% 19.00% 0.07% 0.00% NA
Aus  269 82.20% 17.50% 0.37% 0.00% NA
Indica I  595 97.10% 2.00% 0.84% 0.00% NA
Indica II  465 82.80% 17.00% 0.22% 0.00% NA
Indica III  913 79.20% 20.50% 0.33% 0.00% NA
Indica Intermediate  786 89.90% 9.70% 0.38% 0.00% NA
Temperate Japonica  767 76.70% 23.20% 0.13% 0.00% NA
Tropical Japonica  504 87.90% 12.10% 0.00% 0.00% NA
Japonica Intermediate  241 80.10% 19.90% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 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
vg0431034778 G -> A LOC_Os04g52240.1 upstream_gene_variant ; 268.0bp to feature; MODIFIER silent_mutation Average:40.217; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0431034778 G -> A LOC_Os04g52230.1 downstream_gene_variant ; 3530.0bp to feature; MODIFIER silent_mutation Average:40.217; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0431034778 G -> A LOC_Os04g52230-LOC_Os04g52240 intergenic_region ; MODIFIER silent_mutation Average:40.217; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431034778 NA 9.58E-09 mr1062_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
vg0431034778 7.81E-06 7.81E-06 mr1186_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
vg0431034778 7.58E-06 7.58E-06 mr1445_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
vg0431034778 3.10E-06 3.10E-06 mr1648_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
vg0431034778 9.10E-06 9.10E-06 mr1697_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
vg0431034778 3.59E-06 3.59E-06 mr1756_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