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Detailed information for vg1013526752:

Variant ID: vg1013526752 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13526752
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ACGTATAAAACCCAGATCAGACAATTGGACTGACCTAGATACAGCAGTACCATATACAAAATTGAAGATGATGGATCACACAATTGGACTGACCCAGATA[C/T]
GGCAATACCATATATAAAATTGAAGATGATTCCGTACTCACCTTAATTTTTGTCCATCATCCGAGTTAGACACGTATAAAACATAGATTAGACAATTGGA

Reverse complement sequence

TCCAATTGTCTAATCTATGTTTTATACGTGTCTAACTCGGATGATGGACAAAAATTAAGGTGAGTACGGAATCATCTTCAATTTTATATATGGTATTGCC[G/A]
TATCTGGGTCAGTCCAATTGTGTGATCCATCATCTTCAATTTTGTATATGGTACTGCTGTATCTAGGTCAGTCCAATTGTCTGATCTGGGTTTTATACGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 1.80% 1.40% 0.00% NA
All Indica  2759 94.50% 3.10% 2.39% 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 86.60% 7.20% 6.22% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 91.60% 4.80% 3.56% 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
vg1013526752 C -> T LOC_Os10g26110.1 upstream_gene_variant ; 827.0bp to feature; MODIFIER silent_mutation Average:66.047; most accessible tissue: Callus, score: 74.504 N N N N
vg1013526752 C -> T LOC_Os10g26110-LOC_Os10g26130 intergenic_region ; MODIFIER silent_mutation Average:66.047; most accessible tissue: Callus, score: 74.504 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013526752 2.01E-10 6.61E-11 mr1533 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
vg1013526752 8.79E-12 2.71E-12 mr1980 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
vg1013526752 1.13E-06 2.31E-08 mr1533_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