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Detailed information for vg0813025998:

Variant ID: vg0813025998 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13025998
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: 128. )

Flanking Sequence (100 bp) in Reference Genome:


CTCATCGTTTTCCCCATGATTTTCCCTTCCAGTTCTGTTTTAATTCACCAAATTTAATCTTCATTTAAAAGTCACTGTTTTTATCGAGTTTTGCGAATGC[G/A]
CTCCGATTTTGATAAAAAGGAAAGAGGAGATCGAGTGTATCAAAAGAGATCGAGAAAGATTCGACCAGATTTGATGGGGAGGATTGGTTTTGGCATCGTA

Reverse complement sequence

TACGATGCCAAAACCAATCCTCCCCATCAAATCTGGTCGAATCTTTCTCGATCTCTTTTGATACACTCGATCTCCTCTTTCCTTTTTATCAAAATCGGAG[C/T]
GCATTCGCAAAACTCGATAAAAACAGTGACTTTTAAATGAAGATTAAATTTGGTGAATTAAAACAGAACTGGAAGGGAAAATCATGGGGAAAACGATGAG

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 98.10% 1.90% 0.06% 0.00% NA
All Indica  2759 96.70% 3.20% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.40% 7.20% 0.34% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0813025998 G -> A LOC_Os08g21740.1 downstream_gene_variant ; 1653.0bp to feature; MODIFIER silent_mutation Average:61.404; most accessible tissue: Callus, score: 77.419 N N N N
vg0813025998 G -> A LOC_Os08g21760.1 downstream_gene_variant ; 2057.0bp to feature; MODIFIER silent_mutation Average:61.404; most accessible tissue: Callus, score: 77.419 N N N N
vg0813025998 G -> A LOC_Os08g21740-LOC_Os08g21760 intergenic_region ; MODIFIER silent_mutation Average:61.404; most accessible tissue: Callus, score: 77.419 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813025998 NA 3.66E-07 mr1389 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
vg0813025998 4.13E-06 NA mr1528 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
vg0813025998 NA 1.63E-08 mr1038_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
vg0813025998 NA 2.69E-07 mr1038_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
vg0813025998 NA 7.04E-06 mr1711_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
vg0813025998 NA 9.28E-06 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