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Detailed information for vg0627850120:

Variant ID: vg0627850120 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27850120
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAACCTAGCTATAACGAAACTGTTTATTCATATATTATAACACTATGATCCAAGCATAACAAGTATGCTATAACACTAATAAATACGTTATAACACCAAC[G/A]
AATCGTTTTTTTTTAAGATCTGCCGCTGGATTGATCCATGCATATATCGTTTGCTCAAAGATCGATCATATGTATCATATGCATCTGCTTGATTAATTTG

Reverse complement sequence

CAAATTAATCAAGCAGATGCATATGATACATATGATCGATCTTTGAGCAAACGATATATGCATGGATCAATCCAGCGGCAGATCTTAAAAAAAAACGATT[C/T]
GTTGGTGTTATAACGTATTTATTAGTGTTATAGCATACTTGTTATGCTTGGATCATAGTGTTATAATATATGAATAAACAGTTTCGTTATAGCTAGGTTT

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 91.10% 8.90% 0.00% 0.00% NA
All Indica  2759 85.30% 14.70% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 81.50% 18.50% 0.00% 0.00% NA
Indica III  913 75.50% 24.50% 0.00% 0.00% NA
Indica Intermediate  786 87.90% 12.10% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0627850120 G -> A LOC_Os06g45960.1 upstream_gene_variant ; 1864.0bp to feature; MODIFIER silent_mutation Average:43.148; most accessible tissue: Zhenshan97 flower, score: 62.865 N N N N
vg0627850120 G -> A LOC_Os06g45960-LOC_Os06g45970 intergenic_region ; MODIFIER silent_mutation Average:43.148; most accessible tissue: Zhenshan97 flower, score: 62.865 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627850120 1.88E-06 3.22E-08 mr1341_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
vg0627850120 5.38E-06 5.38E-06 mr1341_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
vg0627850120 NA 1.96E-08 mr1531_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
vg0627850120 NA 1.99E-06 mr1807_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