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Detailed information for vg1013894332:

Variant ID: vg1013894332 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13894332
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCCACCGCCAATTCTCTATCTTTCTGAAGTAGAGAAAGGATATGTGAGGTCAGAGAGCCTACGTATCAATCACCCATAGTGGTGTTTGAAACTCATGAAG[T/C]
TGAAGATTAAGTGACCGCACGTAAAACAAAAAGCTATTAGCACATAATTAATTAAGTCTTAATTATTATAAATTTGACAAATGGATATATTTGATATTTC

Reverse complement sequence

GAAATATCAAATATATCCATTTGTCAAATTTATAATAATTAAGACTTAATTAATTATGTGCTAATAGCTTTTTGTTTTACGTGCGGTCACTTAATCTTCA[A/G]
CTTCATGAGTTTCAAACACCACTATGGGTGATTGATACGTAGGCTCTCTGACCTCACATATCCTTTCTCTACTTCAGAAAGATAGAGAATTGGCGGTGGC

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 93.20% 6.70% 0.13% 0.00% NA
All Indica  2759 89.30% 10.40% 0.22% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 80.90% 19.10% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 9.80% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1013894332 T -> C LOC_Os10g26630.1 downstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:62.941; most accessible tissue: Minghui63 flower, score: 79.334 N N N N
vg1013894332 T -> C LOC_Os10g26620-LOC_Os10g26630 intergenic_region ; MODIFIER silent_mutation Average:62.941; most accessible tissue: Minghui63 flower, score: 79.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013894332 NA 1.47E-06 mr1111 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
vg1013894332 5.39E-06 NA mr1931 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
vg1013894332 NA 1.75E-06 mr1094_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
vg1013894332 NA 1.77E-06 mr1096_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
vg1013894332 NA 9.52E-06 mr1121_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