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Detailed information for vg0507335771:

Variant ID: vg0507335771 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7335771
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


GAGATCCATGTCAGCATATTTTCCTACTTGGAAGAGATTAAATGAAGAGGGAGAGCAAAACTATCTACTAACCTAGAGATAGTCTATAGAGAAAAATGAG[G/A]
CAATGCATTAGAGAGCTATAGATACCCATGTAGACATACCATTGAGGTGGTTTACTATTAATCTAGTCTATTGCTGAGATGCACATATTTTAAGAGCACC

Reverse complement sequence

GGTGCTCTTAAAATATGTGCATCTCAGCAATAGACTAGATTAATAGTAAACCACCTCAATGGTATGTCTACATGGGTATCTATAGCTCTCTAATGCATTG[C/T]
CTCATTTTTCTCTATAGACTATCTCTAGGTTAGTAGATAGTTTTGCTCTCCCTCTTCATTTAATCTCTTCCAAGTAGGAAAATATGCTGACATGGATCTC

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 93.40% 5.90% 0.70% 0.00% NA
All Indica  2759 89.60% 9.30% 1.12% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.90% 10.40% 1.68% 0.00% NA
Indica II  465 78.10% 19.60% 2.37% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 86.80% 12.10% 1.15% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 2.22% 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
vg0507335771 G -> A LOC_Os05g12780.1 upstream_gene_variant ; 638.0bp to feature; MODIFIER silent_mutation Average:57.18; most accessible tissue: Minghui63 root, score: 75.155 N N N N
vg0507335771 G -> A LOC_Os05g12790.1 downstream_gene_variant ; 3550.0bp to feature; MODIFIER silent_mutation Average:57.18; most accessible tissue: Minghui63 root, score: 75.155 N N N N
vg0507335771 G -> A LOC_Os05g12780-LOC_Os05g12790 intergenic_region ; MODIFIER silent_mutation Average:57.18; most accessible tissue: Minghui63 root, score: 75.155 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507335771 8.92E-14 1.46E-10 mr1593 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
vg0507335771 1.03E-12 1.17E-10 mr1593 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
vg0507335771 2.04E-14 1.76E-11 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
vg0507335771 1.67E-12 9.28E-13 mr1593_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