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Detailed information for vg0431516011:

Variant ID: vg0431516011 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31516011
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTTTTATTACTGTAACTTGATTTATCATCTTGAAACATTATTACTTAATATTTTATATTTATAAAAAACAAAATAAATGGTCAAACGTTTGTTAAAAA[G/A]
TCAACGATGTTATATATTAAAAAAACAGAGGTAGTAACTTTTAAAGTTTAAATTTTATTTAAAATATAATAATTTTTTCACTTTTCACATATATTTTCTT

Reverse complement sequence

AAGAAAATATATGTGAAAAGTGAAAAAATTATTATATTTTAAATAAAATTTAAACTTTAAAAGTTACTACCTCTGTTTTTTTAATATATAACATCGTTGA[C/T]
TTTTTAACAAACGTTTGACCATTTATTTTGTTTTTTATAAATATAAAATATTAAGTAATAATGTTTCAAGATGATAAATCAAGTTACAGTAATAAAACAA

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 92.00% 5.70% 0.17% 2.18% NA
All Indica  2759 95.60% 1.70% 0.14% 2.54% NA
All Japonica  1512 86.20% 11.40% 0.20% 2.12% NA
Aus  269 85.10% 14.90% 0.00% 0.00% NA
Indica I  595 95.60% 1.30% 0.50% 2.52% NA
Indica II  465 90.50% 7.10% 0.22% 2.15% NA
Indica III  913 97.80% 0.00% 0.00% 2.19% NA
Indica Intermediate  786 96.10% 0.80% 0.00% 3.18% NA
Temperate Japonica  767 92.70% 2.90% 0.39% 4.04% NA
Tropical Japonica  504 74.80% 25.00% 0.00% 0.20% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431516011 G -> DEL N N silent_mutation Average:44.62; most accessible tissue: Callus, score: 83.839 N N N N
vg0431516011 G -> A LOC_Os04g52900.1 upstream_gene_variant ; 1703.0bp to feature; MODIFIER silent_mutation Average:44.62; most accessible tissue: Callus, score: 83.839 N N N N
vg0431516011 G -> A LOC_Os04g52900.2 upstream_gene_variant ; 1703.0bp to feature; MODIFIER silent_mutation Average:44.62; most accessible tissue: Callus, score: 83.839 N N N N
vg0431516011 G -> A LOC_Os04g52910.1 downstream_gene_variant ; 3232.0bp to feature; MODIFIER silent_mutation Average:44.62; most accessible tissue: Callus, score: 83.839 N N N N
vg0431516011 G -> A LOC_Os04g52900-LOC_Os04g52910 intergenic_region ; MODIFIER silent_mutation Average:44.62; most accessible tissue: Callus, score: 83.839 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431516011 1.16E-06 NA mr1083 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
vg0431516011 9.71E-07 NA mr1226 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
vg0431516011 5.17E-07 NA mr1233 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
vg0431516011 NA 1.78E-07 mr1233 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
vg0431516011 9.30E-07 NA mr1411 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
vg0431516011 4.77E-06 NA mr1800_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