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Detailed information for vg0114208243:

Variant ID: vg0114208243 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14208243
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATGCAACAAGATCTTAGTATAAAGGCAGATTTAACATGTCAATCAAGCATATAAGATAGAAGTAGTTAAATCAGGTAAGGTCGGCTGAAACCCCGATG[G/C]
TACCCTAATCGGCAACCAAAAGCAGGCTAGAGATTGAGATTCTAATCACGACTTATAAGGTCAAACTCAACTGATGCATCTATAAGTATGAAAATAAAGA

Reverse complement sequence

TCTTTATTTTCATACTTATAGATGCATCAGTTGAGTTTGACCTTATAAGTCGTGATTAGAATCTCAATCTCTAGCCTGCTTTTGGTTGCCGATTAGGGTA[C/G]
CATCGGGGTTTCAGCCGACCTTACCTGATTTAACTACTTCTATCTTATATGCTTGATTGACATGTTAAATCTGCCTTTATACTAAGATCTTGTTGCATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.70% 3.00% 7.53% 34.70% NA
All Indica  2759 31.20% 4.90% 10.66% 53.17% NA
All Japonica  1512 95.50% 0.00% 0.66% 3.84% NA
Aus  269 61.70% 1.90% 14.50% 21.93% NA
Indica I  595 32.40% 0.00% 10.59% 56.97% NA
Indica II  465 23.00% 11.80% 10.97% 54.19% NA
Indica III  913 35.00% 5.50% 9.97% 49.51% NA
Indica Intermediate  786 30.80% 3.90% 11.32% 53.94% NA
Temperate Japonica  767 98.40% 0.00% 0.13% 1.43% NA
Tropical Japonica  504 89.50% 0.00% 1.59% 8.93% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 60.40% 0.00% 3.12% 36.46% NA
Intermediate  90 63.30% 2.20% 11.11% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114208243 G -> DEL N N silent_mutation Average:8.287; most accessible tissue: Callus, score: 31.438 N N N N
vg0114208243 G -> C LOC_Os01g25160.1 downstream_gene_variant ; 2236.0bp to feature; MODIFIER silent_mutation Average:8.287; most accessible tissue: Callus, score: 31.438 N N N N
vg0114208243 G -> C LOC_Os01g25150-LOC_Os01g25160 intergenic_region ; MODIFIER silent_mutation Average:8.287; most accessible tissue: Callus, score: 31.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114208243 NA 5.14E-06 mr1448 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
vg0114208243 6.55E-06 2.60E-06 mr1677 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