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Detailed information for vg0116191559:

Variant ID: vg0116191559 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16191559
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AATTGATGGTTTTACATCAACAGAAGGTTTTGCATTCACAACATTTGATTTCGAAGAAGATGCATTCAAAGAAGACATGATGCCAGCAGATTTAAACACA[G/A]
TGTTCTTAAGCTCAGTTTCAATCAAAATTTCACCTCTCCCAGCAGCACCCAAAACAGTAGAAGGATGTCTAGTATGATAAGCATAAGGATCAAAACCTAA

Reverse complement sequence

TTAGGTTTTGATCCTTATGCTTATCATACTAGACATCCTTCTACTGTTTTGGGTGCTGCTGGGAGAGGTGAAATTTTGATTGAAACTGAGCTTAAGAACA[C/T]
TGTGTTTAAATCTGCTGGCATCATGTCTTCTTTGAATGCATCTTCTTCGAAATCAAATGTTGTGAATGCAAAACCTTCTGTTGATGTAAAACCATCAATT

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 94.20% 2.90% 2.81% 0.00% NA
All Indica  2759 90.40% 5.00% 4.68% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 76.30% 11.30% 12.44% 0.00% NA
Indica II  465 92.50% 2.60% 4.95% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 89.10% 7.00% 3.94% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 93.30% 2.20% 4.44% 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
vg0116191559 G -> A LOC_Os01g28894.1 downstream_gene_variant ; 1168.0bp to feature; MODIFIER silent_mutation Average:19.135; most accessible tissue: Callus, score: 30.595 N N N N
vg0116191559 G -> A LOC_Os01g28882.1 intron_variant ; MODIFIER silent_mutation Average:19.135; most accessible tissue: Callus, score: 30.595 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116191559 NA 6.19E-06 mr1712 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