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Detailed information for vg0816363117:

Variant ID: vg0816363117 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16363117
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAAGAGATGCAACCGATGGCTGGATGAATCACCATCAGAAGTGTAGCGCAGGATTGCAAGAGGACGTTAAACTGATCAAGAGTTTGTATATTTTGAAAG[G/A]
CACAATATATGTAGGAAAGGATAGTAAAGTATAATAACAGAATAGCAAAGCTGAATAAATGTTCCTAAGTATGTGTAGCAAATAGCAATCACTGGTTGAG

Reverse complement sequence

CTCAACCAGTGATTGCTATTTGCTACACATACTTAGGAACATTTATTCAGCTTTGCTATTCTGTTATTATACTTTACTATCCTTTCCTACATATATTGTG[C/T]
CTTTCAAAATATACAAACTCTTGATCAGTTTAACGTCCTCTTGCAATCCTGCGCTACACTTCTGATGGTGATTCATCCAGCCATCGGTTGCATCTCTTGT

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 56.50% 43.00% 0.19% 0.34% NA
All Indica  2759 84.50% 14.80% 0.22% 0.47% NA
All Japonica  1512 7.50% 92.30% 0.07% 0.13% NA
Aus  269 69.90% 30.10% 0.00% 0.00% NA
Indica I  595 93.80% 6.10% 0.00% 0.17% NA
Indica II  465 95.10% 4.50% 0.22% 0.22% NA
Indica III  913 72.90% 26.30% 0.11% 0.66% NA
Indica Intermediate  786 84.60% 14.20% 0.51% 0.64% NA
Temperate Japonica  767 1.00% 98.80% 0.13% 0.00% NA
Tropical Japonica  504 14.70% 85.10% 0.00% 0.20% NA
Japonica Intermediate  241 12.90% 86.70% 0.00% 0.41% NA
VI/Aromatic  96 2.10% 96.90% 1.04% 0.00% NA
Intermediate  90 40.00% 57.80% 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
vg0816363117 G -> A LOC_Os08g26875.1 downstream_gene_variant ; 4911.0bp to feature; MODIFIER silent_mutation Average:51.23; most accessible tissue: Callus, score: 68.437 N N N N
vg0816363117 G -> A LOC_Os08g26875-LOC_Os08g26880 intergenic_region ; MODIFIER silent_mutation Average:51.23; most accessible tissue: Callus, score: 68.437 N N N N
vg0816363117 G -> DEL N N silent_mutation Average:51.23; most accessible tissue: Callus, score: 68.437 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816363117 1.05E-06 3.26E-08 mr1167_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
vg0816363117 NA 3.21E-06 mr1726_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