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Detailed information for vg0914657992:

Variant ID: vg0914657992 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 14657992
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGACTTTTAGAAAGTAAACGGGGATTGAAACACATAATGGTAGACTAAATTCACATTTCATATGTCATGTTATAATAGATACTTCCTCCGTTTCACAAT[G/A]
TAAGTCATTCTAGCATTTTTCGCTAGCATCTATATGAATGTGTGAAATGCTAGAATGACATACATTGTGAAACGGATGGAGTAAGAAAAATAAACAATAT

Reverse complement sequence

ATATTGTTTATTTTTCTTACTCCATCCGTTTCACAATGTATGTCATTCTAGCATTTCACACATTCATATAGATGCTAGCGAAAAATGCTAGAATGACTTA[C/T]
ATTGTGAAACGGAGGAAGTATCTATTATAACATGACATATGAAATGTGAATTTAGTCTACCATTATGTGTTTCAATCCCCGTTTACTTTCTAAAAGTCAT

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 92.80% 7.20% 0.02% 0.00% NA
All Indica  2759 95.80% 4.20% 0.00% 0.00% NA
All Japonica  1512 85.70% 14.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 95.50% 4.50% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 73.70% 26.20% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0914657992 G -> A LOC_Os09g24610.1 upstream_gene_variant ; 2711.0bp to feature; MODIFIER silent_mutation Average:44.851; most accessible tissue: Callus, score: 76.786 N N N N
vg0914657992 G -> A LOC_Os09g24620.1 upstream_gene_variant ; 1931.0bp to feature; MODIFIER silent_mutation Average:44.851; most accessible tissue: Callus, score: 76.786 N N N N
vg0914657992 G -> A LOC_Os09g24630.1 downstream_gene_variant ; 3683.0bp to feature; MODIFIER silent_mutation Average:44.851; most accessible tissue: Callus, score: 76.786 N N N N
vg0914657992 G -> A LOC_Os09g24610-LOC_Os09g24620 intergenic_region ; MODIFIER silent_mutation Average:44.851; most accessible tissue: Callus, score: 76.786 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0914657992 NA 2.06E-06 mr1075 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
vg0914657992 NA 5.10E-07 mr1082 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
vg0914657992 NA 1.77E-07 mr1861 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
vg0914657992 NA 1.75E-08 mr1982 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