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Detailed information for vg0815769876:

Variant ID: vg0815769876 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15769876
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: 0.03, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATGGCTGATAGCTTGTTGGCTCTACTTACCAGAAATGCACAAGTTTTACAATGCAAAATGAATGAGGTGGATTAGAAATTCTGAATTGCATTATGGC[G/A]
TGACATCTTGCATGAATAAATGGATAAAAGAGGCACCTCTTTTGCTTCAATTAACTTTGTCTTTTGCGTAGGTGCGGCCAAAACCTTACGTATAAGAGCT

Reverse complement sequence

AGCTCTTATACGTAAGGTTTTGGCCGCACCTACGCAAAAGACAAAGTTAATTGAAGCAAAAGAGGTGCCTCTTTTATCCATTTATTCATGCAAGATGTCA[C/T]
GCCATAATGCAATTCAGAATTTCTAATCCACCTCATTCATTTTGCATTGTAAAACTTGTGCATTTCTGGTAAGTAGAGCCAACAAGCTATCAGCCATTTA

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 85.10% 14.90% 0.00% 0.00% NA
All Indica  2759 95.30% 4.70% 0.00% 0.00% NA
All Japonica  1512 74.70% 25.30% 0.00% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 93.10% 6.90% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 39.70% 60.30% 0.00% 0.00% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg0815769876 G -> A LOC_Os08g25890.1 upstream_gene_variant ; 2911.0bp to feature; MODIFIER silent_mutation Average:38.964; most accessible tissue: Zhenshan97 young leaf, score: 61.964 N N N N
vg0815769876 G -> A LOC_Os08g25880.1 downstream_gene_variant ; 4086.0bp to feature; MODIFIER silent_mutation Average:38.964; most accessible tissue: Zhenshan97 young leaf, score: 61.964 N N N N
vg0815769876 G -> A LOC_Os08g25900.1 intron_variant ; MODIFIER silent_mutation Average:38.964; most accessible tissue: Zhenshan97 young leaf, score: 61.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815769876 NA 5.45E-09 mr1077 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
vg0815769876 NA 3.99E-07 mr1551 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
vg0815769876 NA 4.88E-06 mr1077_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
vg0815769876 NA 1.85E-06 mr1277_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
vg0815769876 NA 4.64E-12 mr1593_2 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
vg0815769876 NA 6.70E-08 mr1642_2 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