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Detailed information for vg0819536015:

Variant ID: vg0819536015 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19536015
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AAACCAGGGTTGTTGTGCAACCTTAGAAACTCTCAATCAATACCACAGGATGCTCATCCAATAGCTAGGGATAGAGATAGGCTAATTTTGCACTTAACCA[C/T]
CTGCCCTTAGCTCTGCTAATCTGTTTTTTTGCAAATCCCCCCAATCCCAGCATCCATCCGCCTGTCCGCCCCGCGCCGTTTCATTTCTGCAGATTCGCCG

Reverse complement sequence

CGGCGAATCTGCAGAAATGAAACGGCGCGGGGCGGACAGGCGGATGGATGCTGGGATTGGGGGGATTTGCAAAAAAACAGATTAGCAGAGCTAAGGGCAG[G/A]
TGGTTAAGTGCAAAATTAGCCTATCTCTATCCCTAGCTATTGGATGAGCATCCTGTGGTATTGATTGAGAGTTTCTAAGGTTGCACAACAACCCTGGTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.20% 31.70% 0.06% 0.00% NA
All Indica  2759 96.80% 3.10% 0.07% 0.00% NA
All Japonica  1512 16.10% 83.90% 0.00% 0.00% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 96.20% 3.70% 0.11% 0.00% NA
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 40.30% 59.70% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 47.90% 51.00% 1.04% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0819536015 C -> T LOC_Os08g31569.1 upstream_gene_variant ; 2866.0bp to feature; MODIFIER silent_mutation Average:63.649; most accessible tissue: Callus, score: 85.636 N N N N
vg0819536015 C -> T LOC_Os08g31569-LOC_Os08g31580 intergenic_region ; MODIFIER silent_mutation Average:63.649; most accessible tissue: Callus, score: 85.636 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819536015 NA 3.79E-06 mr1073 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
vg0819536015 NA 6.19E-06 mr1830 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
vg0819536015 NA 3.65E-06 mr1068_2 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
vg0819536015 NA 2.11E-06 mr1096_2 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
vg0819536015 NA 6.70E-06 mr1211_2 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
vg0819536015 3.67E-06 1.12E-38 mr1224_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
vg0819536015 4.44E-06 NA mr1786_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