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Detailed information for vg0222686622:

Variant ID: vg0222686622 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22686622
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: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCGAGGGGTCCCATCATCGCCTCCTCCCTCGCCGGTGTTGCTTACGCCGCCCATGCCCTCGTTGCTCATGTCTTACTCTGACTTGCACCACATAAATT[G/A]
CATGGGACAATCCTCTAGTTTTATTAAAAGAAAAAAAAAGCTTCATCAATTCCCGTCTCTTGTCCCCGAGTTTTTTTTAACATAAAGAACACTTATCTAT

Reverse complement sequence

ATAGATAAGTGTTCTTTATGTTAAAAAAAACTCGGGGACAAGAGACGGGAATTGATGAAGCTTTTTTTTTCTTTTAATAAAACTAGAGGATTGTCCCATG[C/T]
AATTTATGTGGTGCAAGTCAGAGTAAGACATGAGCAACGAGGGCATGGGCGGCGTAAGCAACACCGGCGAGGGAGGAGGCGATGATGGGACCCCTCGGAC

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 88.10% 8.70% 3.24% 0.00% NA
All Indica  2759 80.00% 14.70% 5.33% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 62.90% 20.70% 16.47% 0.00% NA
Indica II  465 92.50% 5.80% 1.72% 0.00% NA
Indica III  913 83.90% 15.20% 0.88% 0.00% NA
Indica Intermediate  786 80.90% 14.90% 4.20% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 93.30% 2.20% 4.44% 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
vg0222686622 G -> A LOC_Os02g37590.1 upstream_gene_variant ; 656.0bp to feature; MODIFIER silent_mutation Average:64.658; most accessible tissue: Minghui63 young leaf, score: 79.549 N N N N
vg0222686622 G -> A LOC_Os02g37580-LOC_Os02g37590 intergenic_region ; MODIFIER silent_mutation Average:64.658; most accessible tissue: Minghui63 young leaf, score: 79.549 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222686622 6.06E-06 NA mr1929 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
vg0222686622 NA 5.45E-08 mr1124_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
vg0222686622 NA 5.59E-06 mr1222_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
vg0222686622 2.01E-07 NA mr1918_2 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
vg0222686622 1.19E-06 8.31E-06 mr1918_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
vg0222686622 NA 1.04E-08 mr1962_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