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Detailed information for vg0820198596:

Variant ID: vg0820198596 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20198596
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GATATGTTTTTTTTTAAAAAAAATTCGAGATATAAGTTTTCATAAGAAATCAAATAAATCCATTTGTTAAGTTATAATTAATATTTAATTAATCACACGC[T/G]
AAAGATTCATTTCGTTTTGGGTGCCGCTCTTATGCACAGCCAAAGTGCTCCACCGAACGGAGCTAAGTAGTAGCATCTTGTAAAACCAATCCACAACACT

Reverse complement sequence

AGTGTTGTGGATTGGTTTTACAAGATGCTACTACTTAGCTCCGTTCGGTGGAGCACTTTGGCTGTGCATAAGAGCGGCACCCAAAACGAAATGAATCTTT[A/C]
GCGTGTGATTAATTAAATATTAATTATAACTTAACAAATGGATTTATTTGATTTCTTATGAAAACTTATATCTCGAATTTTTTTTAAAAAAAAACATATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.20% 0.40% 0.36% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 97.80% 1.10% 1.06% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.50% 0.17% 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 95.80% 2.20% 1.96% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 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
vg0820198596 T -> G LOC_Os08g32610.1 upstream_gene_variant ; 1109.0bp to feature; MODIFIER silent_mutation Average:53.602; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0820198596 T -> G LOC_Os08g32610-LOC_Os08g32620 intergenic_region ; MODIFIER silent_mutation Average:53.602; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820198596 3.63E-07 3.63E-07 mr1008 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
vg0820198596 4.48E-06 4.49E-06 mr1009 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
vg0820198596 1.95E-08 1.95E-08 mr1067 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
vg0820198596 2.18E-08 1.24E-06 mr1124 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
vg0820198596 2.01E-09 2.01E-09 mr1855 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