Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0223948926:

Variant ID: vg0223948926 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23948926
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAGCAGCAGCGGCTTCGGTGGCAGCAAAGAGGAGGGGTGGTGGCGGTGACCGGCGGCAGCAACTCCCGCGCGTGAGTAACAGATCTGGTGGTGGCGGAC[G/A,T]
GGCTCGGCAGAGTGGGGTGGCGTAGGGGAGCCTAGCTCCTCCCCTCTCCATTTCCGGAGTGGGGTGACAAAGGGGAGTATCGTCTCTCCGGGCTCAGCAG

Reverse complement sequence

CTGCTGAGCCCGGAGAGACGATACTCCCCTTTGTCACCCCACTCCGGAAATGGAGAGGGGAGGAGCTAGGCTCCCCTACGCCACCCCACTCTGCCGAGCC[C/T,A]
GTCCGCCACCACCAGATCTGTTACTCACGCGCGGGAGTTGCTGCCGCCGGTCACCGCCACCACCCCTCCTCTTTGCTGCCACCGAAGCCGCTGCTGCTGG

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 96.30% 3.20% 0.55% 0.00% T: 0.02%
All Indica  2759 99.80% 0.10% 0.00% 0.00% T: 0.04%
All Japonica  1512 89.40% 9.10% 1.59% 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 99.80% 0.10% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 1.30% 0.91% 0.00% NA
Tropical Japonica  504 78.40% 19.20% 2.38% 0.00% NA
Japonica Intermediate  241 85.50% 12.40% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 2.22% 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
vg0223948926 G -> A LOC_Os02g39650.1 upstream_gene_variant ; 2414.0bp to feature; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N
vg0223948926 G -> A LOC_Os02g39660.1 upstream_gene_variant ; 4000.0bp to feature; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N
vg0223948926 G -> A LOC_Os02g39650-LOC_Os02g39660 intergenic_region ; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N
vg0223948926 G -> T LOC_Os02g39650.1 upstream_gene_variant ; 2414.0bp to feature; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N
vg0223948926 G -> T LOC_Os02g39660.1 upstream_gene_variant ; 4000.0bp to feature; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N
vg0223948926 G -> T LOC_Os02g39650-LOC_Os02g39660 intergenic_region ; MODIFIER silent_mutation Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223948926 1.92E-06 1.57E-08 mr1156_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