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Detailed information for vg0826744653:

Variant ID: vg0826744653 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26744653
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AACTTAACTGCTTGTTTGTTGGGCAACTCGAGGAAAAGGATGCTGAGATTAAGAGGAGAATTTGATTTTTAATCTCAGTATCTTGTTTGGTAGAGGTAAT[G/A]
GAAATTGATAGAGAGTTTAGTTAAAGATTAGATCATTAATGATAACGGATGGCTAAAATTTATTTAGGCAAACTAAAGGAGGAATTCTCTCCCAATTACC

Reverse complement sequence

GGTAATTGGGAGAGAATTCCTCCTTTAGTTTGCCTAAATAAATTTTAGCCATCCGTTATCATTAATGATCTAATCTTTAACTAAACTCTCTATCAATTTC[C/T]
ATTACCTCTACCAAACAAGATACTGAGATTAAAAATCAAATTCTCCTCTTAATCTCAGCATCCTTTTCCTCGAGTTGCCCAACAAACAAGCAGTTAAGTT

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 97.70% 1.10% 1.18% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.90% 3.50% 3.64% 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  465 100.00% 0.00% 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 87.20% 6.40% 6.39% 0.00% NA
Tropical Japonica  504 99.20% 0.00% 0.79% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg0826744653 G -> A LOC_Os08g42360.1 upstream_gene_variant ; 2175.0bp to feature; MODIFIER silent_mutation Average:75.273; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0826744653 G -> A LOC_Os08g42370.1 downstream_gene_variant ; 141.0bp to feature; MODIFIER silent_mutation Average:75.273; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0826744653 G -> A LOC_Os08g42370.2 downstream_gene_variant ; 141.0bp to feature; MODIFIER silent_mutation Average:75.273; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0826744653 G -> A LOC_Os08g42370.3 downstream_gene_variant ; 141.0bp to feature; MODIFIER silent_mutation Average:75.273; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0826744653 G -> A LOC_Os08g42360-LOC_Os08g42370 intergenic_region ; MODIFIER silent_mutation Average:75.273; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826744653 2.40E-06 NA mr1310_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