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Detailed information for vg0329925779:

Variant ID: vg0329925779 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29925779
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAAATTACATATGGCTCGGGGTCTATTTATACCCGAGAATTACAAGATATGACCATACCGGACACGACTATTATCTCTAACAAACTCTAAGATACCAT[A/G]
AGTCTTTGCGGCAGACTTTTGCCCACATTTATTTATAAGGAATTTACATAAGATATCCTAATTAATAGATACAATTACCTTTCCAGGACTCCATCCGTGT

Reverse complement sequence

ACACGGATGGAGTCCTGGAAAGGTAATTGTATCTATTAATTAGGATATCTTATGTAAATTCCTTATAAATAAATGTGGGCAAAAGTCTGCCGCAAAGACT[T/C]
ATGGTATCTTAGAGTTTGTTAGAGATAATAGTCGTGTCCGGTATGGTCATATCTTGTAATTCTCGGGTATAAATAGACCCCGAGCCATATGTAATTTAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.90% 14.00% 0.13% 0.00% NA
All Indica  2759 76.40% 23.40% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 69.70% 29.70% 0.50% 0.00% NA
Indica II  465 67.30% 32.50% 0.22% 0.00% NA
Indica III  913 82.60% 17.30% 0.11% 0.00% NA
Indica Intermediate  786 79.60% 20.20% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0329925779 A -> G LOC_Os03g52110.1 upstream_gene_variant ; 1329.0bp to feature; MODIFIER silent_mutation Average:27.192; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0329925779 A -> G LOC_Os03g52120.1 upstream_gene_variant ; 1786.0bp to feature; MODIFIER silent_mutation Average:27.192; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0329925779 A -> G LOC_Os03g52110-LOC_Os03g52120 intergenic_region ; MODIFIER silent_mutation Average:27.192; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329925779 NA 2.33E-06 mr1536 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
vg0329925779 3.83E-06 3.93E-06 mr1745 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