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Detailed information for vg0132820574:

Variant ID: vg0132820574 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32820574
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGTATAGCGTGGAGCATTGTAAATGCTGTTAGAGCAAGTTTAATAATAGAGCCAAGTATGAGCTTATAGCTTATATTAGGTTAACATATATAGTAGAT[C/T]
AGCCATAAGGTTATCTCTATTTTTCTCCTCCTCTCTCTATCTCTCACCTTTGCATTTAATGTATTTATCTTGAAGTATGTGAATGGCTAGCTCTTGTATA

Reverse complement sequence

TATACAAGAGCTAGCCATTCACATACTTCAAGATAAATACATTAAATGCAAAGGTGAGAGATAGAGAGAGGAGGAGAAAAATAGAGATAACCTTATGGCT[G/A]
ATCTACTATATATGTTAACCTAATATAAGCTATAAGCTCATACTTGGCTCTATTATTAAACTTGCTCTAACAGCATTTACAATGCTCCACGCTATACAGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.20% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 82.80% 15.90% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 75.60% 22.00% 2.35% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 73.90% 25.30% 0.83% 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
vg0132820574 C -> T LOC_Os01g56820.1 upstream_gene_variant ; 1122.0bp to feature; MODIFIER silent_mutation Average:56.975; most accessible tissue: Callus, score: 89.159 N N N N
vg0132820574 C -> T LOC_Os01g56830.1 upstream_gene_variant ; 1651.0bp to feature; MODIFIER silent_mutation Average:56.975; most accessible tissue: Callus, score: 89.159 N N N N
vg0132820574 C -> T LOC_Os01g56820.2 upstream_gene_variant ; 1122.0bp to feature; MODIFIER silent_mutation Average:56.975; most accessible tissue: Callus, score: 89.159 N N N N
vg0132820574 C -> T LOC_Os01g56820-LOC_Os01g56830 intergenic_region ; MODIFIER silent_mutation Average:56.975; most accessible tissue: Callus, score: 89.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0132820574 8.00E-06 8.95E-06 mr1049 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
vg0132820574 NA 2.68E-06 mr1050 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
vg0132820574 NA 7.34E-06 mr1126 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
vg0132820574 NA 1.29E-06 mr1252 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
vg0132820574 NA 7.69E-06 mr1576 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
vg0132820574 NA 3.72E-06 mr1821 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