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Detailed information for vg0434562918:

Variant ID: vg0434562918 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34562918
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.30, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATGATAATTTAACATGTTTATATTTAAAAAACTCTTAAATTATAAAAACTATAAAGATATAGCATGTTTGCATGATGTTTAAATGTGATGATTGTTA[A/G]
TGGATGATGATGTGGCATCTTGTTAATTAGTGGATTAATGGATGATGATGTGATATCTTTGTATGAGCTTAAGGAATTAGTGGGGGTAACTTTATAGTAA

Reverse complement sequence

TTACTATAAAGTTACCCCCACTAATTCCTTAAGCTCATACAAAGATATCACATCATCATCCATTAATCCACTAATTAACAAGATGCCACATCATCATCCA[T/C]
TAACAATCATCACATTTAAACATCATGCAAACATGCTATATCTTTATAGTTTTTATAATTTAAGAGTTTTTTAAATATAAACATGTTAAATTATCATCCA

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 56.60% 43.30% 0.06% 0.00% NA
All Indica  2759 94.60% 5.30% 0.11% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 96.50% 3.20% 0.34% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 87.80% 12.20% 0.00% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg0434562918 A -> G LOC_Os04g58020.1 upstream_gene_variant ; 3359.0bp to feature; MODIFIER silent_mutation Average:29.186; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0434562918 A -> G LOC_Os04g58040.1 upstream_gene_variant ; 3874.0bp to feature; MODIFIER silent_mutation Average:29.186; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0434562918 A -> G LOC_Os04g58030.1 downstream_gene_variant ; 1466.0bp to feature; MODIFIER silent_mutation Average:29.186; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0434562918 A -> G LOC_Os04g58020-LOC_Os04g58030 intergenic_region ; MODIFIER silent_mutation Average:29.186; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434562918 NA 3.47E-10 mr1151 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
vg0434562918 1.39E-06 3.06E-06 mr1713 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