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Detailed information for vg0825151239:

Variant ID: vg0825151239 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25151239
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


CGGTTAGCATCCATATAAAATTATATATATTTTTAATATGATTTTACTTAAAATTTATTAAATAGTTTTCTCATTATCTTTAGATTTTGAAAGTTCAAAC[C/A]
TTATCATCCTCTTATTTCTAGTTTTATAATTTTTAAAAGTCACACCAGTTGCTACCCTTTACTTTTGTCATATTATTCTTCATTTGATTGCTCGATCTAC

Reverse complement sequence

GTAGATCGAGCAATCAAATGAAGAATAATATGACAAAAGTAAAGGGTAGCAACTGGTGTGACTTTTAAAAATTATAAAACTAGAAATAAGAGGATGATAA[G/T]
GTTTGAACTTTCAAAATCTAAAGATAATGAGAAAACTATTTAATAAATTTTAAGTAAAATCATATTAAAAATATATATAATTTTATATGGATGCTAACCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 11.00% 2.52% 0.00% NA
All Indica  2759 77.90% 18.10% 4.02% 0.00% NA
All Japonica  1512 98.90% 0.80% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 70.80% 19.00% 10.25% 0.00% NA
Indica II  465 46.00% 48.20% 5.81% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 76.50% 20.60% 2.93% 0.00% NA
Temperate Japonica  767 98.30% 1.30% 0.39% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 11.10% 3.33% 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
vg0825151239 C -> A LOC_Os08g39720.1 upstream_gene_variant ; 4265.0bp to feature; MODIFIER silent_mutation Average:29.18; most accessible tissue: Callus, score: 53.213 N N N N
vg0825151239 C -> A LOC_Os08g39730.1 upstream_gene_variant ; 3919.0bp to feature; MODIFIER silent_mutation Average:29.18; most accessible tissue: Callus, score: 53.213 N N N N
vg0825151239 C -> A LOC_Os08g39720-LOC_Os08g39730 intergenic_region ; MODIFIER silent_mutation Average:29.18; most accessible tissue: Callus, score: 53.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825151239 NA 3.38E-06 mr1212 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
vg0825151239 6.33E-06 NA mr1699 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
vg0825151239 1.33E-06 8.83E-09 mr1699 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
vg0825151239 1.92E-09 NA mr1874 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
vg0825151239 1.79E-08 6.77E-11 mr1874 Ind_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
vg0825151239 1.93E-06 NA mr1699_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
vg0825151239 2.27E-06 9.40E-11 mr1699_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
vg0825151239 5.30E-08 NA mr1874_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
vg0825151239 3.67E-07 9.42E-12 mr1874_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