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Detailed information for vg0503364634:

Variant ID: vg0503364634 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3364634
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGTTGCCTGTATCTCATGCCATCTACACGATGTTGCCTAGCAGCCTAGTAGCATATCTCATGCCATCTACTCCATTGTTTTTCACACGTTTTTCGAAC[T/G]
GTTAAATGTTGCATTTTTTGTAAAAAACATCTTATAGGAAAGTGTTTCAAACAAATCATATTAATTCATTTTTAAGCTAATACTTAATTAATCATATGTT

Reverse complement sequence

AACATATGATTAATTAAGTATTAGCTTAAAAATGAATTAATATGATTTGTTTGAAACACTTTCCTATAAGATGTTTTTTACAAAAAATGCAACATTTAAC[A/C]
GTTCGAAAAACGTGTGAAAAACAATGGAGTAGATGGCATGAGATATGCTACTAGGCTGCTAGGCAACATCGTGTAGATGGCATGAGATACAGGCAACAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.70% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.90% 5.10% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0503364634 T -> G LOC_Os05g06540.1 upstream_gene_variant ; 4374.0bp to feature; MODIFIER silent_mutation Average:52.493; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0503364634 T -> G LOC_Os05g06540.2 upstream_gene_variant ; 4374.0bp to feature; MODIFIER silent_mutation Average:52.493; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0503364634 T -> G LOC_Os05g06530.1 downstream_gene_variant ; 58.0bp to feature; MODIFIER silent_mutation Average:52.493; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0503364634 T -> G LOC_Os05g06530.2 downstream_gene_variant ; 58.0bp to feature; MODIFIER silent_mutation Average:52.493; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0503364634 T -> G LOC_Os05g06530-LOC_Os05g06540 intergenic_region ; MODIFIER silent_mutation Average:52.493; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503364634 2.36E-06 1.31E-07 mr1695_2 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
vg0503364634 NA 2.47E-07 mr1705_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