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Detailed information for vg0719509692:

Variant ID: vg0719509692 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19509692
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTTGACACCTATTTATAGTTGTTTATAGTAGCTCTTACATATTCATCTTACGACTTTGATTATCCGTTGATCCCTAATTTACTAATCACCATGACTC[G/A]
CATAAAAAAATATGTACTACATAGAGTTTAGGACAGCTGAAATTGATAAATTATCTGATTTATGTGATAGCTATTTGAGGGTATAAACGAATGAATTGAC

Reverse complement sequence

GTCAATTCATTCGTTTATACCCTCAAATAGCTATCACATAAATCAGATAATTTATCAATTTCAGCTGTCCTAAACTCTATGTAGTACATATTTTTTTATG[C/T]
GAGTCATGGTGATTAGTAAATTAGGGATCAACGGATAATCAAAGTCGTAAGATGAATATGTAAGAGCTACTATAAACAACTATAAATAGGTGTCAAAATT

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 90.70% 9.30% 0.00% 0.00% NA
All Indica  2759 86.70% 13.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 77.50% 22.50% 0.00% 0.00% NA
Indica Intermediate  786 85.10% 14.90% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0719509692 G -> A LOC_Os07g32670.1 downstream_gene_variant ; 4533.0bp to feature; MODIFIER silent_mutation Average:26.585; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0719509692 G -> A LOC_Os07g32670-LOC_Os07g32680 intergenic_region ; MODIFIER silent_mutation Average:26.585; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719509692 6.65E-07 NA mr1248_2 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
vg0719509692 NA 6.63E-06 mr1406_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
vg0719509692 6.59E-06 NA mr1423_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
vg0719509692 8.66E-06 NA mr1800_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