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Detailed information for vg0321132765:

Variant ID: vg0321132765 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21132765
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCTTTTCTGGGGATTAGGCCGCATTTCGCTCTATTCCGCCGTATCTTCTTCCTCAAACCCCAGCCAAACAAAAGCAAACCATGCGTAGTTGGGGCAGCC[A/G]
TATTTCAACTGAGGGGAACCTTGAGCCAAAAATATTTCTCCATGCCTTTTAAAACTTCAAATAAGGGTTGGCATGCAAATTGGTTTTATGTGCAAAATCC

Reverse complement sequence

GGATTTTGCACATAAAACCAATTTGCATGCCAACCCTTATTTGAAGTTTTAAAAGGCATGGAGAAATATTTTTGGCTCAAGGTTCCCCTCAGTTGAAATA[T/C]
GGCTGCCCCAACTACGCATGGTTTGCTTTTGTTTGGCTGGGGTTTGAGGAAGAAGATACGGCGGAATAGAGCGAAATGCGGCCTAATCCCCAGAAAAGCT

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 63.00% 36.50% 0.51% 0.00% NA
All Indica  2759 95.70% 3.60% 0.76% 0.00% NA
All Japonica  1512 1.80% 98.20% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 97.50% 1.30% 1.18% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 5.60% 1.78% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 4.20% 95.80% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 50.00% 46.70% 3.33% 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
vg0321132765 A -> G LOC_Os03g38076.1 downstream_gene_variant ; 2880.0bp to feature; MODIFIER silent_mutation Average:43.419; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N
vg0321132765 A -> G LOC_Os03g38070.1 intron_variant ; MODIFIER silent_mutation Average:43.419; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321132765 NA 1.32E-19 mr1588 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
vg0321132765 1.42E-07 4.24E-77 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
vg0321132765 NA 2.87E-06 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
vg0321132765 2.36E-12 6.11E-128 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
vg0321132765 7.80E-08 2.78E-14 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
vg0321132765 2.28E-07 NA mr1718_2 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
vg0321132765 1.32E-12 4.36E-157 mr1750_2 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
vg0321132765 1.99E-08 7.56E-19 mr1750_2 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