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Detailed information for vg0918113499:

Variant ID: vg0918113499 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18113499
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TATCAAGCTATACTTGCAGCCCGTTTGAAGGCCAAATACTTCTCTAATAAGGATTTTGATGGAGGTATTTGTGAAATCATCATCTATGTGCAGTATAGAT[A/T]
TTACCTAGTATATTTGTGCACACTTTTTTTTTCACACGTTTAATCACATACAGGCATGCCATTTTTTCAGTCTCATGCTATAGAGATCTGCTATTGATAC

Reverse complement sequence

GTATCAATAGCAGATCTCTATAGCATGAGACTGAAAAAATGGCATGCCTGTATGTGATTAAACGTGTGAAAAAAAAAGTGTGCACAAATATACTAGGTAA[T/A]
ATCTATACTGCACATAGATGATGATTTCACAAATACCTCCATCAAAATCCTTATTAGAGAAGTATTTGGCCTTCAAACGGGCTGCAAGTATAGCTTGATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.50% 19.40% 0.11% 0.00% NA
All Indica  2759 77.90% 21.90% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 21.20% 78.80% 0.00% 0.00% NA
Indica I  595 49.10% 50.80% 0.17% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 94.60% 5.40% 0.00% 0.00% NA
Indica Intermediate  786 70.90% 28.80% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 78.10% 1.04% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0918113499 A -> T LOC_Os09g29790.1 upstream_gene_variant ; 4186.0bp to feature; MODIFIER silent_mutation Average:36.184; most accessible tissue: Callus, score: 75.372 N N N N
vg0918113499 A -> T LOC_Os09g29810.1 upstream_gene_variant ; 1626.0bp to feature; MODIFIER silent_mutation Average:36.184; most accessible tissue: Callus, score: 75.372 N N N N
vg0918113499 A -> T LOC_Os09g29800.1 intron_variant ; MODIFIER silent_mutation Average:36.184; most accessible tissue: Callus, score: 75.372 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918113499 NA 2.91E-09 mr1138 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
vg0918113499 NA 4.05E-07 mr1707 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
vg0918113499 5.07E-06 5.66E-10 mr1728 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
vg0918113499 1.41E-06 2.96E-12 mr1728 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
vg0918113499 NA 8.13E-09 mr1860 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
vg0918113499 NA 1.93E-06 mr1008_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
vg0918113499 NA 9.77E-09 mr1138_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
vg0918113499 4.42E-06 NA mr1707_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
vg0918113499 4.34E-07 7.73E-08 mr1707_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
vg0918113499 1.86E-06 NA mr1728_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
vg0918113499 4.71E-07 1.58E-13 mr1728_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
vg0918113499 NA 1.36E-10 mr1860_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