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Detailed information for vg0506871977:

Variant ID: vg0506871977 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6871977
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


AATTAATAGCTAGATATTTTGCTTTATTTTTTCTTAGAATTTCTCTAATTTATTAGAGCGCCACTTGGCAGCCTAGGAGCGTTTGTAGAGATGTCATGTG[A/G]
CGGCTTAGGAGCATTTGTAGAAAGTTTTATAAACTTTTAGTATTATTTTTTTCTTAGAATTTTTCTAATTTATTAGAGCGCCACTTGACAGTCTAGGAGC

Reverse complement sequence

GCTCCTAGACTGTCAAGTGGCGCTCTAATAAATTAGAAAAATTCTAAGAAAAAAATAATACTAAAAGTTTATAAAACTTTCTACAAATGCTCCTAAGCCG[T/C]
CACATGACATCTCTACAAACGCTCCTAGGCTGCCAAGTGGCGCTCTAATAAATTAGAGAAATTCTAAGAAAAAATAAAGCAAAATATCTAGCTATTAATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.30% 9.20% 6.14% 42.30% NA
All Indica  2759 11.90% 12.80% 6.74% 68.54% NA
All Japonica  1512 95.30% 0.50% 2.84% 1.32% NA
Aus  269 31.60% 23.40% 20.45% 24.54% NA
Indica I  595 5.00% 7.90% 6.05% 81.01% NA
Indica II  465 20.40% 7.10% 5.38% 67.10% NA
Indica III  913 10.70% 17.70% 7.67% 63.86% NA
Indica Intermediate  786 13.40% 14.20% 7.00% 65.39% NA
Temperate Japonica  767 98.40% 0.10% 0.26% 1.17% NA
Tropical Japonica  504 94.40% 0.60% 3.37% 1.59% NA
Japonica Intermediate  241 87.10% 1.70% 9.96% 1.24% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 57.80% 12.20% 6.67% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0506871977 A -> DEL N N silent_mutation Average:43.24; most accessible tissue: Callus, score: 60.287 N N N N
vg0506871977 A -> G LOC_Os05g12020.1 upstream_gene_variant ; 1850.0bp to feature; MODIFIER silent_mutation Average:43.24; most accessible tissue: Callus, score: 60.287 N N N N
vg0506871977 A -> G LOC_Os05g12010.1 downstream_gene_variant ; 3736.0bp to feature; MODIFIER silent_mutation Average:43.24; most accessible tissue: Callus, score: 60.287 N N N N
vg0506871977 A -> G LOC_Os05g12010-LOC_Os05g12020 intergenic_region ; MODIFIER silent_mutation Average:43.24; most accessible tissue: Callus, score: 60.287 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506871977 9.67E-11 2.52E-40 mr1039 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
vg0506871977 3.36E-08 7.45E-10 mr1039 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
vg0506871977 NA 3.60E-11 mr1514 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
vg0506871977 NA 2.74E-08 mr1593 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
vg0506871977 1.31E-08 1.67E-41 mr1632 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
vg0506871977 5.10E-07 2.05E-12 mr1632 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
vg0506871977 2.80E-09 1.31E-48 mr1873 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
vg0506871977 8.35E-06 4.46E-10 mr1873 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
vg0506871977 5.76E-12 1.38E-42 mr1039_2 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
vg0506871977 2.21E-08 6.99E-10 mr1039_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
vg0506871977 4.43E-10 4.77E-20 mr1514_2 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
vg0506871977 5.75E-07 8.01E-08 mr1514_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
vg0506871977 NA 1.65E-08 mr1593_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
vg0506871977 9.26E-15 4.43E-55 mr1632_2 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
vg0506871977 8.65E-11 4.03E-15 mr1632_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
vg0506871977 1.96E-07 7.72E-07 mr1750_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
vg0506871977 1.18E-08 1.86E-40 mr1873_2 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
vg0506871977 2.91E-06 4.19E-08 mr1873_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