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Detailed information for vg0234783509:

Variant ID: vg0234783509 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 34783509
Reference Allele: GAlternative Allele: T,GATTGTCTGGCTA
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TGCCGTTTGGAGTTGCGTTTAGCTGCTGTAGTAGTTTTTTTCCTAGTTTCAGTTTTTGTTTTGCTTTTTTTCTTTTCCCCTGGTATAAGCCGGTCTGGCT[G/T,GATTGTCTGGCTA]
ATTGTGTTGTTGTAACAAAAACTTTTTTTCTTTCCAATATATTGATGATTAATCCTTTTGCGTGTTCGTGAAAAAGAAACAAAATGATATGAGCCATAGA

Reverse complement sequence

TCTATGGCTCATATCATTTTGTTTCTTTTTCACGAACACGCAAAAGGATTAATCATCAATATATTGGAAAGAAAAAAAGTTTTTGTTACAACAACACAAT[C/A,TAGCCAGACAATC]
AGCCAGACCGGCTTATACCAGGGGAAAAGAAAAAAAGCAAAACAAAAACTGAAACTAGGAAAAAAACTACTACAGCAGCTAAACGCAACTCCAAACGGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 7.00% 0.02% 0.00% GATTGTCTGGCTA: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% GATTGTCTGGCTA: 0.04%
All Japonica  1512 78.40% 21.50% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.00% GATTGTCTGGCTA: 0.11%
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 69.40% 30.50% 0.13% 0.00% NA
Tropical Japonica  504 92.70% 7.30% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0234783509 G -> T LOC_Os02g56740.1 upstream_gene_variant ; 647.0bp to feature; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N
vg0234783509 G -> T LOC_Os02g56740.2 upstream_gene_variant ; 647.0bp to feature; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N
vg0234783509 G -> T LOC_Os02g56730-LOC_Os02g56740 intergenic_region ; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N
vg0234783509 G -> GATTGTCTGGCTA LOC_Os02g56740.1 upstream_gene_variant ; 646.0bp to feature; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N
vg0234783509 G -> GATTGTCTGGCTA LOC_Os02g56740.2 upstream_gene_variant ; 646.0bp to feature; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N
vg0234783509 G -> GATTGTCTGGCTA LOC_Os02g56730-LOC_Os02g56740 intergenic_region ; MODIFIER silent_mutation Average:77.08; most accessible tissue: Callus, score: 90.793 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234783509 5.57E-06 NA mr1930 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
vg0234783509 3.95E-06 3.95E-06 mr1930 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