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Detailed information for vg0800104112:

Variant ID: vg0800104112 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 104112
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: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTTTTAAACAATGTTTGACATTTATCTTATTCAATTTTTTTTACAAATATAAAAATACCATGCTTAAAGAATAAATCAAGTCACAATAAAATTAAT[G/A]
ATAATTACATAATTTTTTTAAATAAATTGAATGGTTAAACGCTGATAAAAGATTAATTGTATTATATATTAAAATACGGAGGGAGTATATATTAATCCTA

Reverse complement sequence

TAGGATTAATATATACTCCCTCCGTATTTTAATATATAATACAATTAATCTTTTATCAGCGTTTAACCATTCAATTTATTTAAAAAAATTATGTAATTAT[C/T]
ATTAATTTTATTGTGACTTGATTTATTCTTTAAGCATGGTATTTTTATATTTGTAAAAAAAATTGAATAAGATAAATGTCAAACATTGTTTAAAAAATCA

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 85.80% 14.20% 0.00% 0.00% NA
All Indica  2759 80.70% 19.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 53.90% 46.10% 0.00% 0.00% NA
Indica I  595 79.30% 20.70% 0.00% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 70.60% 29.40% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 15.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0800104112 G -> A LOC_Os08g01160.1 upstream_gene_variant ; 4335.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800104112 G -> A LOC_Os08g01150.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800104112 1.93E-06 2.95E-08 mr1277 Ind_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
vg0800104112 6.70E-07 2.55E-09 mr1746 Ind_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
vg0800104112 NA 1.76E-06 mr1277_2 Ind_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
vg0800104112 2.36E-06 NA mr1746_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
vg0800104112 6.78E-08 4.01E-12 mr1746_2 Ind_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