Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0805724088:

Variant ID: vg0805724088 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5724088
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.31, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGCTTCTCCATCATCCTTTGGGCATTATGAAACCGTGAATGGCTTTTGGAATATCTCTGATGCTGCGGCTAGACTGCCAATAGTAAACAGCTTCAGTT[A/G]
GTGCTACAGAATGGTTGATCCTCCTTGCGTGTCATGCTTGAGCTTGCGTTGTTGGCATAGAATCGTTTCTGTGAACTGGCTGTTTGCATAAAATCCATAG

Reverse complement sequence

CTATGGATTTTATGCAAACAGCCAGTTCACAGAAACGATTCTATGCCAACAACGCAAGCTCAAGCATGACACGCAAGGAGGATCAACCATTCTGTAGCAC[T/C]
AACTGAAGCTGTTTACTATTGGCAGTCTAGCCGCAGCATCAGAGATATTCCAAAAGCCATTCACGGTTTCATAATGCCCAAAGGATGATGGAGAAGCTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.20% 49.70% 0.11% 0.00% NA
All Indica  2759 24.80% 75.00% 0.18% 0.00% NA
All Japonica  1512 94.40% 5.60% 0.00% 0.00% NA
Aus  269 45.40% 54.60% 0.00% 0.00% NA
Indica I  595 9.60% 90.40% 0.00% 0.00% NA
Indica II  465 36.10% 63.90% 0.00% 0.00% NA
Indica III  913 27.90% 72.10% 0.00% 0.00% NA
Indica Intermediate  786 26.00% 73.40% 0.64% 0.00% NA
Temperate Japonica  767 96.70% 3.30% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 84.20% 15.80% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0805724088 A -> G LOC_Os08g09900.1 upstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:67.123; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0805724088 A -> G LOC_Os08g09920.1 upstream_gene_variant ; 3937.0bp to feature; MODIFIER silent_mutation Average:67.123; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0805724088 A -> G LOC_Os08g09920.2 upstream_gene_variant ; 3937.0bp to feature; MODIFIER silent_mutation Average:67.123; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0805724088 A -> G LOC_Os08g09910.1 downstream_gene_variant ; 267.0bp to feature; MODIFIER silent_mutation Average:67.123; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0805724088 A -> G LOC_Os08g09910-LOC_Os08g09920 intergenic_region ; MODIFIER silent_mutation Average:67.123; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805724088 NA 1.20E-14 mr1751 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
vg0805724088 NA 3.72E-06 mr1751 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