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Detailed information for vg0111338686:

Variant ID: vg0111338686 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11338686
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CACAAATTGAATTAATTTTTTTAATCCTTTTTAAATGGGCTTTAATTAGATTTAATCTTGTAAAATTCATAATAAATTCATTTGAAGTCAGAATGAGGCC[G/A]
TTCAAGTCTCAAAATTCATCTAAAATTATGATCTACATGTTTGTTTACTTTTTATGTATTGTCTATTTGGTTTTTATTAGTCTTTTTCCTCGTTTTGCGT

Reverse complement sequence

ACGCAAAACGAGGAAAAAGACTAATAAAAACCAAATAGACAATACATAAAAAGTAAACAAACATGTAGATCATAATTTTAGATGAATTTTGAGACTTGAA[C/T]
GGCCTCATTCTGACTTCAAATGAATTTATTATGAATTTTACAAGATTAAATCTAATTAAAGCCCATTTAAAAAGGATTAAAAAAATTAATTCAATTTGTG

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% 1.80% 1.48% 0.00% NA
All Indica  2759 94.40% 3.10% 2.50% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.40% 8.60% 8.07% 0.00% NA
Indica II  465 94.80% 3.40% 1.72% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 96.10% 2.40% 1.53% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 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
vg0111338686 G -> A LOC_Os01g19960.1 downstream_gene_variant ; 3755.0bp to feature; MODIFIER silent_mutation Average:14.787; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0111338686 G -> A LOC_Os01g19960-LOC_Os01g19970 intergenic_region ; MODIFIER silent_mutation Average:14.787; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111338686 2.26E-06 NA mr1195_2 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
vg0111338686 2.36E-06 NA mr1580_2 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
vg0111338686 5.13E-06 NA mr1825_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