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Detailed information for vg0819016766:

Variant ID: vg0819016766 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19016766
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCTAATTTTTTGGGATTTTGGTTAAAAAAAACTGGTCCAACAGATTCCCAAAAGAGCTCTGGACGTTTTGGAGTTCCCATCTCCAATTTTCTCGGTAC[G/A]
TGTATTTGAGGGCGAGAGAACGACTCCCAATCCCCTCCTTCCACTCGAATTTCTAAAAAAACGATTTCTATTGGTAGTTTAACAATTTCTAAAAAAAACT

Reverse complement sequence

AGTTTTTTTTAGAAATTGTTAAACTACCAATAGAAATCGTTTTTTTAGAAATTCGAGTGGAAGGAGGGGATTGGGAGTCGTTCTCTCGCCCTCAAATACA[C/T]
GTACCGAGAAAATTGGAGATGGGAACTCCAAAACGTCCAGAGCTCTTTTGGGAATCTGTTGGACCAGTTTTTTTTAACCAAAATCCCAAAAAATTAGGAT

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 85.30% 14.70% 0.00% 0.00% NA
All Indica  2759 81.30% 18.70% 0.00% 0.00% NA
All Japonica  1512 88.30% 11.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.50% 5.50% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 70.40% 29.60% 0.00% 0.00% NA
Indica Intermediate  786 76.20% 23.80% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 67.90% 32.10% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0819016766 G -> A LOC_Os08g30790.1 downstream_gene_variant ; 766.0bp to feature; MODIFIER silent_mutation Average:47.44; most accessible tissue: Zhenshan97 root, score: 77.417 N N N N
vg0819016766 G -> A LOC_Os08g30800.1 downstream_gene_variant ; 481.0bp to feature; MODIFIER silent_mutation Average:47.44; most accessible tissue: Zhenshan97 root, score: 77.417 N N N N
vg0819016766 G -> A LOC_Os08g30790.3 downstream_gene_variant ; 766.0bp to feature; MODIFIER silent_mutation Average:47.44; most accessible tissue: Zhenshan97 root, score: 77.417 N N N N
vg0819016766 G -> A LOC_Os08g30790.2 downstream_gene_variant ; 766.0bp to feature; MODIFIER silent_mutation Average:47.44; most accessible tissue: Zhenshan97 root, score: 77.417 N N N N
vg0819016766 G -> A LOC_Os08g30790-LOC_Os08g30800 intergenic_region ; MODIFIER silent_mutation Average:47.44; most accessible tissue: Zhenshan97 root, score: 77.417 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819016766 NA 5.67E-06 mr1039 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
vg0819016766 9.29E-08 9.28E-08 mr1266 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
vg0819016766 9.75E-06 1.83E-07 mr1345 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
vg0819016766 NA 5.69E-06 mr1695 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
vg0819016766 NA 3.69E-08 mr1852 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
vg0819016766 NA 3.32E-06 mr1866 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
vg0819016766 1.33E-08 1.33E-08 mr1873 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