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Detailed information for vg0114147236:

Variant ID: vg0114147236 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14147236
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.09, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CTATTTTTCAGAGTTTACTTAGGGCTTCAACTCCAAAATTTAGCTACAGGAGTTGGTTCTGGAGTAGAGTTATGGAGCTTCCTAAACTCAGCTCTACCTC[T/C]
CTAGTTTATTTTGTGAGAGAGCTCTACCCAGCTCCGCTCCCCTTTTAGGTAAAGCTGAAACTGTTTGGCTGAGCTCCAGCTCCAGGAGGAGAGATAGGGT

Reverse complement sequence

ACCCTATCTCTCCTCCTGGAGCTGGAGCTCAGCCAAACAGTTTCAGCTTTACCTAAAAGGGGAGCGGAGCTGGGTAGAGCTCTCTCACAAAATAAACTAG[A/G]
GAGGTAGAGCTGAGTTTAGGAAGCTCCATAACTCTACTCCAGAACCAACTCCTGTAGCTAAATTTTGGAGTTGAAGCCCTAAGTAAACTCTGAAAAATAG

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 58.80% 29.40% 0.21% 11.60% NA
All Indica  2759 37.60% 42.70% 0.33% 19.43% NA
All Japonica  1512 95.40% 4.60% 0.00% 0.00% NA
Aus  269 68.80% 31.20% 0.00% 0.00% NA
Indica I  595 59.50% 39.80% 0.17% 0.50% NA
Indica II  465 45.60% 12.70% 0.00% 41.72% NA
Indica III  913 16.00% 61.20% 0.22% 22.56% NA
Indica Intermediate  786 41.30% 41.00% 0.76% 16.92% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 89.70% 10.30% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 46.90% 0.00% 1.04% NA
Intermediate  90 73.30% 13.30% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114147236 T -> DEL N N silent_mutation Average:26.709; most accessible tissue: Callus, score: 72.702 N N N N
vg0114147236 T -> C LOC_Os01g25070.1 upstream_gene_variant ; 2753.0bp to feature; MODIFIER silent_mutation Average:26.709; most accessible tissue: Callus, score: 72.702 N N N N
vg0114147236 T -> C LOC_Os01g25065-LOC_Os01g25070 intergenic_region ; MODIFIER silent_mutation Average:26.709; most accessible tissue: Callus, score: 72.702 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114147236 NA 7.82E-06 mr1064 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
vg0114147236 NA 1.21E-07 mr1193 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
vg0114147236 1.23E-06 4.27E-08 mr1637 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
vg0114147236 NA 1.34E-10 mr1519_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