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Detailed information for vg0220758243:

Variant ID: vg0220758243 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20758243
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCCTCATACTATGCAAATACCGGAATCGCGACATCAAATGTCGACAGTTGCGCGCCAGGTAGGGGATCTTTTGGTGCTTCAAGGTTTCGATGAGATG[G/A]
GTTTAAGAGATGGATTCTCCGACAACGAGCTACTCGACGACTTCAGCTGAGGGGGAGATCCAACCTAACCAGATCGGAACCATCATCGTCATTGACAACT

Reverse complement sequence

AGTTGTCAATGACGATGATGGTTCCGATCTGGTTAGGTTGGATCTCCCCCTCAGCTGAAGTCGTCGAGTAGCTCGTTGTCGGAGAATCCATCTCTTAAAC[C/T]
CATCTCATCGAAACCTTGAAGCACCAAAAGATCCCCTACCTGGCGCGCAACTGTCGACATTTGATGTCGCGATTCCGGTATTTGCATAGTATGAGGATCG

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 67.70% 31.80% 0.42% 0.08% NA
All Indica  2759 49.30% 50.50% 0.18% 0.07% NA
All Japonica  1512 96.60% 2.60% 0.73% 0.00% NA
Aus  269 77.30% 21.90% 0.00% 0.74% NA
Indica I  595 72.90% 26.90% 0.17% 0.00% NA
Indica II  465 64.90% 34.80% 0.22% 0.00% NA
Indica III  913 29.40% 70.50% 0.11% 0.00% NA
Indica Intermediate  786 45.30% 54.20% 0.25% 0.25% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 93.30% 5.80% 0.99% 0.00% NA
Japonica Intermediate  241 94.60% 3.30% 2.07% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 83.30% 13.30% 3.33% 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
vg0220758243 G -> A LOC_Os02g34610.1 upstream_gene_variant ; 4823.0bp to feature; MODIFIER silent_mutation Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0220758243 G -> A LOC_Os02g34620.1 upstream_gene_variant ; 10.0bp to feature; MODIFIER silent_mutation Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0220758243 G -> A LOC_Os02g34610-LOC_Os02g34620 intergenic_region ; MODIFIER silent_mutation Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0220758243 G -> DEL N N silent_mutation Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220758243 4.00E-06 NA mr1099_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
vg0220758243 4.27E-06 4.52E-06 mr1099_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