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Detailed information for vg0228934167:

Variant ID: vg0228934167 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28934167
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTTACGCTATTTATGTCTAACATTTAACTATTTGTCTTATTTGAAATTTTTTTATGATTACTATTTTATATTTTTATTGTTATTAGATAATAAAACAT[A/G]
AATAGTACTTTATGTGTGACTATTTTTTTAAATTTTTTTATAAATTTTTCAAATAAGACGGATGGTTAAACTTTTGAGGTAGTACATGCTCTCACACAGA

Reverse complement sequence

TCTGTGTGAGAGCATGTACTACCTCAAAAGTTTAACCATCCGTCTTATTTGAAAAATTTATAAAAAAATTTAAAAAAATAGTCACACATAAAGTACTATT[T/C]
ATGTTTTATTATCTAATAACAATAAAAATATAAAATAGTAATCATAAAAAAATTTCAAATAAGACAAATAGTTAAATGTTAGACATAAATAGCGTAAAAC

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 81.40% 18.50% 0.04% 0.00% NA
All Indica  2759 93.80% 6.20% 0.00% 0.00% NA
All Japonica  1512 56.10% 43.80% 0.13% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 90.10% 9.90% 0.00% 0.00% NA
Temperate Japonica  767 24.50% 75.20% 0.26% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 67.20% 32.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0228934167 A -> G LOC_Os02g47390.1 upstream_gene_variant ; 2157.0bp to feature; MODIFIER silent_mutation Average:53.481; most accessible tissue: Callus, score: 85.432 N N N N
vg0228934167 A -> G LOC_Os02g47400.1 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:53.481; most accessible tissue: Callus, score: 85.432 N N N N
vg0228934167 A -> G LOC_Os02g47400.2 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:53.481; most accessible tissue: Callus, score: 85.432 N N N N
vg0228934167 A -> G LOC_Os02g47390-LOC_Os02g47400 intergenic_region ; MODIFIER silent_mutation Average:53.481; most accessible tissue: Callus, score: 85.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228934167 NA 2.35E-07 mr1708 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
vg0228934167 NA 1.06E-08 mr1189_2 Jap_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