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Detailed information for vg0227089280:

Variant ID: vg0227089280 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27089280
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTGTATAGCCCAGAGTTTTCATAACACAAGGGAGAGATCACACTAAGCTTCCCCTTTTCGGGTTTGCAGCCCAGCTCGTGAGGCAAGGTCACGCTGCT[G/A]
CTGTAGGATCGTAAATGATCTTTCCCACCTCAAAAGCTAGCCAATGAGGGATGGGCTCCCCCACTTATATATTAAGTTTCTTGTCCTTCTATAACCAATG

Reverse complement sequence

CATTGGTTATAGAAGGACAAGAAACTTAATATATAAGTGGGGGAGCCCATCCCTCATTGGCTAGCTTTTGAGGTGGGAAAGATCATTTACGATCCTACAG[C/T]
AGCAGCGTGACCTTGCCTCACGAGCTGGGCTGCAAACCCGAAAAGGGGAAGCTTAGTGTGATCTCTCCCTTGTGTTATGAAAACTCTGGGCTATACAGAC

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 93.30% 5.60% 1.08% 0.00% NA
All Indica  2759 99.50% 0.40% 0.04% 0.00% NA
All Japonica  1512 80.20% 16.50% 3.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 71.20% 23.90% 4.95% 0.00% NA
Tropical Japonica  504 97.60% 1.80% 0.60% 0.00% NA
Japonica Intermediate  241 72.20% 24.10% 3.73% 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
vg0227089280 G -> A LOC_Os02g44704.1 upstream_gene_variant ; 1858.0bp to feature; MODIFIER silent_mutation Average:66.618; most accessible tissue: Callus, score: 84.367 N N N N
vg0227089280 G -> A LOC_Os02g44704.2 upstream_gene_variant ; 1778.0bp to feature; MODIFIER silent_mutation Average:66.618; most accessible tissue: Callus, score: 84.367 N N N N
vg0227089280 G -> A LOC_Os02g44710.1 downstream_gene_variant ; 2573.0bp to feature; MODIFIER silent_mutation Average:66.618; most accessible tissue: Callus, score: 84.367 N N N N
vg0227089280 G -> A LOC_Os02g44704-LOC_Os02g44710 intergenic_region ; MODIFIER silent_mutation Average:66.618; most accessible tissue: Callus, score: 84.367 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227089280 NA 5.27E-10 mr1691 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
vg0227089280 1.76E-06 5.96E-07 mr1994_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
vg0227089280 4.07E-06 8.96E-07 mr1994_2 Jap_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