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Detailed information for vg0211612218:

Variant ID: vg0211612218 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11612218
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


TACAAAACCAAGCATTTTACACCCTCAATTGTTTATACCGGACAAATAACCCCCCTCAACACTGTTTCGAGTGGTTTTAACTTGAACGTGCACACGTGGC[G/A]
CCAACGTGGAAATTCAGTCAACAAAAAAAATAAAAAAACTTCCCAGGGGCCCACCTGTCATACCCCTCCCTCAACCTAATCCTTCCCTGTCGCGCAATCT

Reverse complement sequence

AGATTGCGCGACAGGGAAGGATTAGGTTGAGGGAGGGGTATGACAGGTGGGCCCCTGGGAAGTTTTTTTATTTTTTTTGTTGACTGAATTTCCACGTTGG[C/T]
GCCACGTGTGCACGTTCAAGTTAAAACCACTCGAAACAGTGTTGAGGGGGGTTATTTGTCCGGTATAAACAATTGAGGGTGTAAAATGCTTGGTTTTGTA

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 92.80% 6.50% 0.66% 0.00% NA
All Indica  2759 88.10% 10.80% 1.09% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 71.60% 24.90% 3.44% 0.00% NA
Indica III  913 85.20% 14.20% 0.55% 0.00% NA
Indica Intermediate  786 92.50% 6.60% 0.89% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 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 93.30% 6.70% 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
vg0211612218 G -> A LOC_Os02g19830.1 upstream_gene_variant ; 4437.0bp to feature; MODIFIER silent_mutation Average:63.103; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N
vg0211612218 G -> A LOC_Os02g19820-LOC_Os02g19830 intergenic_region ; MODIFIER silent_mutation Average:63.103; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211612218 NA 7.25E-06 mr1129 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
vg0211612218 1.38E-08 2.81E-09 mr1818 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
vg0211612218 NA 1.81E-09 mr1855 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
vg0211612218 NA 5.77E-08 mr1317_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
vg0211612218 NA 4.27E-06 mr1818_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
vg0211612218 NA 1.65E-07 mr1855_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
vg0211612218 NA 8.03E-07 mr1897_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
vg0211612218 NA 2.26E-06 mr1914_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