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Detailed information for vg0524686199:

Variant ID: vg0524686199 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24686199
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AATAATGATAATTATGATGATAGATGGTCCTTCCTTTTTAATGCTATTATTGATGGGTTATGTCTCCAGGAGTTACAGATGTCTGGTTGGAAATTTACTT[G/A]
GGCAAACAATTTAGTGAATCCAACATATGAGAAACTTGATAGGGTTTTAATGTCCACGGAGTGGGAACATAAATTTCCTTTATCTTCTGTGGTGGCTCTT

Reverse complement sequence

AAGAGCCACCACAGAAGATAAAGGAAATTTATGTTCCCACTCCGTGGACATTAAAACCCTATCAAGTTTCTCATATGTTGGATTCACTAAATTGTTTGCC[C/T]
AAGTAAATTTCCAACCAGACATCTGTAACTCCTGGAGACATAACCCATCAATAATAGCATTAAAAAGGAAGGACCATCTATCATCATAATTATCATTATT

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 98.70% 0.70% 0.57% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.00% 2.20% 1.79% 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 92.20% 4.30% 3.52% 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  96 100.00% 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
vg0524686199 G -> A LOC_Os05g42210.1 downstream_gene_variant ; 3571.0bp to feature; MODIFIER silent_mutation Average:24.252; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0524686199 G -> A LOC_Os05g42210-LOC_Os05g42220 intergenic_region ; MODIFIER silent_mutation Average:24.252; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524686199 NA 1.36E-06 mr1100_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
vg0524686199 NA 4.42E-06 mr1128_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
vg0524686199 3.17E-07 9.58E-08 mr1705_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
vg0524686199 NA 9.73E-06 mr1913_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