Search for Variation information by Variation ID:

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

Detailed information for vg0627455814:

Variant ID: vg0627455814 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27455814
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAATTCAACAATATATGATTTACTTATCTAACAATCTTTATAAGTTATACACCCTATGGTAACAAATATTGTTTGATTTTTTTAAAAAAACTTAATAAAT[G/A]
CAGGAAAAACTAATTTAATATTTTCGAGGATACGTATATATGCACCGGCGCTCTGAGGGTGTGTTTGAGGAGAAAAAAAGAGAATATTAAGAAAAAAATA

Reverse complement sequence

TATTTTTTTCTTAATATTCTCTTTTTTTCTCCTCAAACACACCCTCAGAGCGCCGGTGCATATATACGTATCCTCGAAAATATTAAATTAGTTTTTCCTG[C/T]
ATTTATTAAGTTTTTTTAAAAAAATCAAACAATATTTGTTACCATAGGGTGTATAACTTATAAAGATTGTTAGATAAGTAAATCATATATTGTTGAATTC

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 96.50% 2.70% 0.78% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.20% 8.40% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 79.40% 16.40% 4.17% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 0.40% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0627455814 G -> A LOC_Os06g45410.1 upstream_gene_variant ; 1096.0bp to feature; MODIFIER silent_mutation Average:29.53; most accessible tissue: Callus, score: 57.767 N N N N
vg0627455814 G -> A LOC_Os06g45390-LOC_Os06g45410 intergenic_region ; MODIFIER silent_mutation Average:29.53; most accessible tissue: Callus, score: 57.767 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627455814 3.95E-06 2.76E-06 mr1354_2 Jap_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
vg0627455814 NA 6.03E-06 mr1588_2 Jap_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