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Detailed information for vg0416982091:

Variant ID: vg0416982091 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16982091
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


GGGATTCAATATGTTCAAGGATGATGCGATTTGCCTTGCTCAGAGACAACGGCCTTCCGAACCTTCGGCGACGATCGCGAACCACGCTTCGGGAACCTCC[G/A]
GAACGACAGAAGCTACGCGAAGCACACAAGCAAAGCTACAAGCCTATAAAGAAGCAATAACAATACATAAAAAGAAAGCACAGGGTTCTTTAGGTTATAG

Reverse complement sequence

CTATAACCTAAAGAACCCTGTGCTTTCTTTTTATGTATTGTTATTGCTTCTTTATAGGCTTGTAGCTTTGCTTGTGTGCTTCGCGTAGCTTCTGTCGTTC[C/T]
GGAGGTTCCCGAAGCGTGGTTCGCGATCGTCGCCGAAGGTTCGGAAGGCCGTTGTCTCTGAGCAAGGCAAATCGCATCATCCTTGAACATATTGAATCCC

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 96.70% 1.30% 1.97% 0.00% NA
All Indica  2759 96.90% 1.30% 1.78% 0.00% NA
All Japonica  1512 97.00% 1.10% 1.92% 0.00% NA
Aus  269 91.40% 3.30% 5.20% 0.00% NA
Indica I  595 87.60% 5.00% 7.39% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 99.00% 0.60% 0.38% 0.00% NA
Temperate Japonica  767 95.30% 1.60% 3.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 1.70% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0416982091 G -> A LOC_Os04g28670.1 upstream_gene_variant ; 931.0bp to feature; MODIFIER silent_mutation Average:29.126; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0416982091 G -> A LOC_Os04g28680.1 upstream_gene_variant ; 4079.0bp to feature; MODIFIER silent_mutation Average:29.126; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0416982091 G -> A LOC_Os04g28650.1 downstream_gene_variant ; 4496.0bp to feature; MODIFIER silent_mutation Average:29.126; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0416982091 G -> A LOC_Os04g28660.1 downstream_gene_variant ; 1665.0bp to feature; MODIFIER silent_mutation Average:29.126; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0416982091 G -> A LOC_Os04g28660-LOC_Os04g28670 intergenic_region ; MODIFIER silent_mutation Average:29.126; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416982091 2.01E-06 2.01E-06 mr1987 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