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Detailed information for vg0324100933:

Variant ID: vg0324100933 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24100933
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:


CCGAGCCGATTGACTTCTCACCGGCCGATTAATATAACCTAAAAGGTATTCCTTTACGTGGAGGAATCAAAACTGGAGGAGAGCTAAGATATTCCTTAAT[A/G]
CTATCCAAAGCTTTCTGCTGCTTTGCCCCCCAAGCAAACTTTTGATCGGCTTTCAATCTTAGCAATGGTGTAAAAGGCTCTAACCTTCCAGACAAATTAG

Reverse complement sequence

CTAATTTGTCTGGAAGGTTAGAGCCTTTTACACCATTGCTAAGATTGAAAGCCGATCAAAAGTTTGCTTGGGGGGCAAAGCAGCAGAAAGCTTTGGATAG[T/C]
ATTAAGGAATATCTTAGCTCTCCTCCAGTTTTGATTCCTCCACGTAAAGGAATACCTTTTAGGTTATATTAATCGGCCGGTGAGAAGTCAATCGGCTCGG

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 42.30% 3.20% 24.46% 30.05% NA
All Indica  2759 5.90% 5.10% 39.62% 49.37% NA
All Japonica  1512 99.10% 0.00% 0.40% 0.46% NA
Aus  269 77.00% 1.90% 10.41% 10.78% NA
Indica I  595 8.60% 3.20% 24.87% 63.36% NA
Indica II  465 3.40% 3.90% 30.32% 62.37% NA
Indica III  913 2.10% 8.70% 56.85% 32.42% NA
Indica Intermediate  786 9.90% 3.10% 36.26% 50.76% NA
Temperate Japonica  767 99.50% 0.00% 0.26% 0.26% NA
Tropical Japonica  504 99.00% 0.00% 0.40% 0.60% NA
Japonica Intermediate  241 98.30% 0.00% 0.83% 0.83% NA
VI/Aromatic  96 79.20% 4.20% 13.54% 3.12% NA
Intermediate  90 57.80% 3.30% 17.78% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0324100933 A -> DEL N N silent_mutation Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224 N N N N
vg0324100933 A -> G LOC_Os03g43210.1 downstream_gene_variant ; 2493.0bp to feature; MODIFIER silent_mutation Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224 N N N N
vg0324100933 A -> G LOC_Os03g43220.1 intron_variant ; MODIFIER silent_mutation Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324100933 NA 3.90E-41 mr1509 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
vg0324100933 NA 4.04E-24 mr1571 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
vg0324100933 NA 3.56E-81 mr1718 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
vg0324100933 5.63E-06 3.00E-07 mr1718 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
vg0324100933 4.38E-06 NA mr1750 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
vg0324100933 2.78E-10 3.92E-12 mr1750 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
vg0324100933 7.32E-07 7.32E-07 mr1987 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