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Detailed information for vg0219817547:

Variant ID: vg0219817547 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19817547
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, G: 0.41, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCCAAGATCATATGCTGACTGTACATTCATGCTTTTTTTTTATACATAACTGGACATTCATACTTACTATGTTTCATTTACGCATAGTACTTTATTGC[A/G]
CGAGCAATTTTGAAGTCCTTGTGGAGGTACCACTTTTTCTATTATAAATTTGGTACCTCATAGTACACTAAATTTTTTATACCTCATGATATCTCCTTAA

Reverse complement sequence

TTAAGGAGATATCATGAGGTATAAAAAATTTAGTGTACTATGAGGTACCAAATTTATAATAGAAAAAGTGGTACCTCCACAAGGACTTCAAAATTGCTCG[T/C]
GCAATAAAGTACTATGCGTAAATGAAACATAGTAAGTATGAATGTCCAGTTATGTATAAAAAAAAAGCATGAATGTACAGTCAGCATATGATCTTGGACA

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 52.30% 47.10% 0.08% 0.51% NA
All Indica  2759 85.80% 13.50% 0.11% 0.54% NA
All Japonica  1512 1.70% 98.00% 0.00% 0.26% NA
Aus  269 18.60% 81.40% 0.00% 0.00% NA
Indica I  595 81.50% 17.50% 0.17% 0.84% NA
Indica II  465 83.00% 16.30% 0.22% 0.43% NA
Indica III  913 92.90% 6.90% 0.00% 0.22% NA
Indica Intermediate  786 82.60% 16.50% 0.13% 0.76% NA
Temperate Japonica  767 1.20% 98.40% 0.00% 0.39% NA
Tropical Japonica  504 1.60% 98.20% 0.00% 0.20% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 0.00% 100.00% 0.00% 0.00% NA
Intermediate  90 33.30% 60.00% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0219817547 A -> G LOC_Os02g33360.1 upstream_gene_variant ; 3141.0bp to feature; MODIFIER silent_mutation Average:51.418; most accessible tissue: Callus, score: 85.372 N N N N
vg0219817547 A -> G LOC_Os02g33340-LOC_Os02g33360 intergenic_region ; MODIFIER silent_mutation Average:51.418; most accessible tissue: Callus, score: 85.372 N N N N
vg0219817547 A -> DEL N N silent_mutation Average:51.418; most accessible tissue: Callus, score: 85.372 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219817547 NA 7.69E-10 mr1151 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
vg0219817547 NA 3.67E-13 mr1183 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
vg0219817547 NA 2.85E-31 mr1225 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
vg0219817547 NA 6.87E-18 mr1255 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
vg0219817547 NA 6.60E-13 mr1503 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
vg0219817547 NA 3.96E-06 mr1881 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
vg0219817547 NA 1.44E-12 mr1138_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
vg0219817547 NA 4.17E-33 mr1161_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
vg0219817547 NA 1.11E-20 mr1164_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
vg0219817547 NA 1.44E-09 mr1172_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
vg0219817547 NA 2.33E-17 mr1180_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
vg0219817547 NA 1.33E-06 mr1180_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
vg0219817547 NA 3.46E-20 mr1183_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
vg0219817547 NA 7.24E-06 mr1519_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
vg0219817547 3.98E-07 NA mr1707_2 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
vg0219817547 3.33E-06 NA mr1707_2 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
vg0219817547 NA 6.50E-09 mr1851_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
vg0219817547 3.58E-06 NA mr1860_2 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
vg0219817547 1.42E-06 NA mr1860_2 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