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Detailed information for vg0205700559:

Variant ID: vg0205700559 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5700559
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


AATCATATTGATGCATGCAAGCAATGTGATTGGGAGGTTTGATGGTATAAGATTTAAAACAAATCAATTTTATAAGACCAAGAGATGATAGTTAATGTAT[G/A]
CATGCATGTACGCTTTATATTACTCCCTCCATTTACTTTTGATAGTCATATTTCTAAATCTGAAAAATTTATTTTTGGTAGGCATATTTCAATTCAACAA

Reverse complement sequence

TTGTTGAATTGAAATATGCCTACCAAAAATAAATTTTTCAGATTTAGAAATATGACTATCAAAAGTAAATGGAGGGAGTAATATAAAGCGTACATGCATG[C/T]
ATACATTAACTATCATCTCTTGGTCTTATAAAATTGATTTGTTTTAAATCTTATACCATCAAACCTCCCAATCACATTGCTTGCATGCATCAATATGATT

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 62.30% 37.60% 0.06% 0.00% NA
All Indica  2759 37.60% 62.30% 0.07% 0.00% NA
All Japonica  1512 98.70% 1.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 32.60% 67.40% 0.00% 0.00% NA
Indica II  465 35.50% 64.50% 0.00% 0.00% NA
Indica III  913 33.70% 66.00% 0.22% 0.00% NA
Indica Intermediate  786 47.10% 52.90% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0205700559 G -> A LOC_Os02g10770.2 upstream_gene_variant ; 2725.0bp to feature; MODIFIER silent_mutation Average:46.48; most accessible tissue: Callus, score: 69.425 N N N N
vg0205700559 G -> A LOC_Os02g10770-LOC_Os02g10780 intergenic_region ; MODIFIER silent_mutation Average:46.48; most accessible tissue: Callus, score: 69.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205700559 4.56E-06 NA mr1006 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
vg0205700559 6.95E-07 2.88E-06 mr1037 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
vg0205700559 6.53E-06 NA mr1052 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
vg0205700559 NA 8.14E-07 mr1053 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
vg0205700559 NA 1.28E-06 mr1761 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
vg0205700559 NA 6.08E-06 mr1705_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