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Detailed information for vg0111652887:

Variant ID: vg0111652887 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11652887
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CCTATACTTCTAGTATACATAATATACATACATCCTAGCTATAAGATTAACTAGCTAATACCCTTATTCCGATGCCCTCCTGGTACTTCGAGAAGCCACC[C/T]
CCTACTGCCGAGTTTCTTACGACAGCCCATCATGACCATACAACCGGGGCTAAATACGAAGGAATACCCTCCCCAGGGAATTAACTAAGGACTATATACA

Reverse complement sequence

TGTATATAGTCCTTAGTTAATTCCCTGGGGAGGGTATTCCTTCGTATTTAGCCCCGGTTGTATGGTCATGATGGGCTGTCGTAAGAAACTCGGCAGTAGG[G/A]
GGTGGCTTCTCGAAGTACCAGGAGGGCATCGGAATAAGGGTATTAGCTAGTTAATCTTATAGCTAGGATGTATGTATATTATGTATACTAGAAGTATAGG

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 93.80% 6.20% 0.02% 0.00% NA
All Indica  2759 89.50% 10.50% 0.04% 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 89.40% 10.40% 0.17% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 88.50% 11.50% 0.00% 0.00% NA
Indica Intermediate  786 87.20% 12.80% 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 96.70% 3.30% 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
vg0111652887 C -> T LOC_Os01g20880.1 upstream_gene_variant ; 2251.0bp to feature; MODIFIER silent_mutation Average:53.251; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0111652887 C -> T LOC_Os01g20870.1 downstream_gene_variant ; 4913.0bp to feature; MODIFIER silent_mutation Average:53.251; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0111652887 C -> T LOC_Os01g20870-LOC_Os01g20880 intergenic_region ; MODIFIER silent_mutation Average:53.251; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111652887 4.91E-06 NA mr1790 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
vg0111652887 NA 8.06E-07 mr1045_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
vg0111652887 NA 5.73E-06 mr1220_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
vg0111652887 NA 3.51E-06 mr1480_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
vg0111652887 NA 8.49E-06 mr1820_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
vg0111652887 NA 2.76E-08 mr1968_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