Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0421232041:

Variant ID: vg0421232041 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21232041
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTAGATCTACAATATTATGCATTAGACCTGTAGTATTGTGGTAAATTTGATGCTATTGTGATACACCCTCTTAAGTCTGTAGTTTAATGTAAGTTTGG[G/A]
TAAAATTGTAATACTGTCATAAATTTAGATCAAAATTTGTGCTTTTCTCATACACCCTATAAAAATTATAATTATTGTTTTGCGATAGTATGGTAAGGTG

Reverse complement sequence

CACCTTACCATACTATCGCAAAACAATAATTATAATTTTTATAGGGTGTATGAGAAAAGCACAAATTTTGATCTAAATTTATGACAGTATTACAATTTTA[C/T]
CCAAACTTACATTAAACTACAGACTTAAGAGGGTGTATCACAATAGCATCAAATTTACCACAATACTACAGGTCTAATGCATAATATTGTAGATCTACAA

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 97.20% 2.80% 0.00% 0.00% NA
All Indica  2759 95.70% 4.30% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 94.40% 5.60% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 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 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0421232041 G -> A LOC_Os04g34930.1 upstream_gene_variant ; 1287.0bp to feature; MODIFIER silent_mutation Average:65.359; most accessible tissue: Callus, score: 86.703 N N N N
vg0421232041 G -> A LOC_Os04g34930.3 upstream_gene_variant ; 1706.0bp to feature; MODIFIER silent_mutation Average:65.359; most accessible tissue: Callus, score: 86.703 N N N N
vg0421232041 G -> A LOC_Os04g34930.2 upstream_gene_variant ; 1287.0bp to feature; MODIFIER silent_mutation Average:65.359; most accessible tissue: Callus, score: 86.703 N N N N
vg0421232041 G -> A LOC_Os04g34940.1 downstream_gene_variant ; 497.0bp to feature; MODIFIER silent_mutation Average:65.359; most accessible tissue: Callus, score: 86.703 N N N N
vg0421232041 G -> A LOC_Os04g34930-LOC_Os04g34940 intergenic_region ; MODIFIER silent_mutation Average:65.359; most accessible tissue: Callus, score: 86.703 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421232041 NA 3.43E-06 mr1217 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
vg0421232041 3.99E-06 3.99E-06 mr1845 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
vg0421232041 NA 1.79E-06 mr1248_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