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Detailed information for vg0116027186:

Variant ID: vg0116027186 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16027186
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCTTCTGAGAGAACCAGTGTTATGTGCCGACTTTTTTTTTAAGTCTTTTGTTTCGTAGCTTTGTTTTCTGTGTTTGTATAAGACTCTGTATACTGTTT[G/A,T]
GGCTTTCTTCCAAAGCCGGGTCAATGAAAATTTGATCTATTTCAAAAAAAAAATGTTCAATTGACTAAATTTTATAAAATCGTTTTACACGTCTAAATGT

Reverse complement sequence

ACATTTAGACGTGTAAAACGATTTTATAAAATTTAGTCAATTGAACATTTTTTTTTTGAAATAGATCAAATTTTCATTGACCCGGCTTTGGAAGAAAGCC[C/T,A]
AAACAGTATACAGAGTCTTATACAAACACAGAAAACAAAGCTACGAAACAAAAGACTTAAAAAAAAAGTCGGCACATAACACTGGTTCTCTCAGAAGCAT

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 79.10% 20.40% 0.25% 0.00% T: 0.23%
All Indica  2759 69.10% 30.10% 0.43% 0.00% T: 0.40%
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 91.80% 8.10% 0.17% 0.00% NA
Indica II  465 55.30% 44.10% 0.43% 0.00% T: 0.22%
Indica III  913 59.60% 40.10% 0.22% 0.00% T: 0.11%
Indica Intermediate  786 71.10% 26.80% 0.89% 0.00% T: 1.15%
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 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0116027186 G -> T LOC_Os01g28640.1 upstream_gene_variant ; 1647.0bp to feature; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0116027186 G -> T LOC_Os01g28650.1 upstream_gene_variant ; 3021.0bp to feature; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0116027186 G -> T LOC_Os01g28640-LOC_Os01g28650 intergenic_region ; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0116027186 G -> A LOC_Os01g28640.1 upstream_gene_variant ; 1647.0bp to feature; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0116027186 G -> A LOC_Os01g28650.1 upstream_gene_variant ; 3021.0bp to feature; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N
vg0116027186 G -> A LOC_Os01g28640-LOC_Os01g28650 intergenic_region ; MODIFIER silent_mutation Average:72.984; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116027186 3.48E-06 1.13E-07 mr1405 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
vg0116027186 NA 8.85E-06 mr1519 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
vg0116027186 NA 1.54E-06 mr1762_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