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Detailed information for vg1109206941:

Variant ID: vg1109206941 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9206941
Reference Allele: GAlternative Allele: A
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: 318. )

Flanking Sequence (100 bp) in Reference Genome:


AAATAAGCGGACGGAAAGTTTTAAGTACCCAAGCAACATACCTCGAGTCTTTGATGTTGAGTTTTCATATACTACCTGTTGGAAATATGGTCATATATCG[G/A]
CATATTTTAATCCAAAATGTTAAGACAATAATCATGGCATAAACAGTGTTGGATGATCTAGTGACAACATGTAGCATAACCAGTAGCATGCTAAAGGTAT

Reverse complement sequence

ATACCTTTAGCATGCTACTGGTTATGCTACATGTTGTCACTAGATCATCCAACACTGTTTATGCCATGATTATTGTCTTAACATTTTGGATTAAAATATG[C/T]
CGATATATGACCATATTTCCAACAGGTAGTATATGAAAACTCAACATCAAAGACTCGAGGTATGTTGCTTGGGTACTTAAAACTTTCCGTCCGCTTATTT

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 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 97.70% 2.30% 0.00% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 92.30% 7.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 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 95.60% 4.40% 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
vg1109206941 G -> A LOC_Os11g16600.1 upstream_gene_variant ; 1694.0bp to feature; MODIFIER silent_mutation Average:31.353; most accessible tissue: Callus, score: 47.322 N N N N
vg1109206941 G -> A LOC_Os11g16610.1 downstream_gene_variant ; 1131.0bp to feature; MODIFIER silent_mutation Average:31.353; most accessible tissue: Callus, score: 47.322 N N N N
vg1109206941 G -> A LOC_Os11g16600-LOC_Os11g16610 intergenic_region ; MODIFIER silent_mutation Average:31.353; most accessible tissue: Callus, score: 47.322 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109206941 2.05E-06 2.05E-06 mr1102 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