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Detailed information for vg1114869295:

Variant ID: vg1114869295 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14869295
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TTATATTACCGCTGTATAATCATTTCCTTTGCAGGCTAACCTTGGTTGTTTTCACTTTTCGTTGTGAAAACAGGGTAGTGCATGACTGGTTTCAACCTGC[T/C]
GGAAAACTTCAAAGAAAATCCAGAAGCTTTCTTCCGGAGCTTCAGGCCGCAAGTCGTTGCTCCGCAGAAAACTCTACCGACACCCACGGGATAAAATAAA

Reverse complement sequence

TTTATTTTATCCCGTGGGTGTCGGTAGAGTTTTCTGCGGAGCAACGACTTGCGGCCTGAAGCTCCGGAAGAAAGCTTCTGGATTTTCTTTGAAGTTTTCC[A/G]
GCAGGTTGAAACCAGTCATGCACTACCCTGTTTTCACAACGAAAAGTGAAAACAACCAAGGTTAGCCTGCAAAGGAAATGATTATACAGCGGTAATATAA

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 36.30% 32.30% 22.28% 9.08% NA
All Indica  2759 4.20% 53.10% 29.61% 13.08% NA
All Japonica  1512 97.20% 0.70% 1.52% 0.60% NA
Aus  269 1.50% 12.30% 67.29% 18.96% NA
Indica I  595 4.90% 33.80% 36.64% 24.71% NA
Indica II  465 2.40% 48.40% 36.13% 13.12% NA
Indica III  913 2.20% 74.00% 17.96% 5.81% NA
Indica Intermediate  786 7.30% 46.10% 33.97% 12.72% NA
Temperate Japonica  767 96.90% 0.50% 1.69% 0.91% NA
Tropical Japonica  504 97.00% 1.00% 1.79% 0.20% NA
Japonica Intermediate  241 98.30% 0.80% 0.41% 0.41% NA
VI/Aromatic  96 90.60% 1.00% 6.25% 2.08% NA
Intermediate  90 44.40% 20.00% 28.89% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1114869295 T -> DEL N N silent_mutation Average:9.812; most accessible tissue: Callus, score: 42.522 N N N N
vg1114869295 T -> C LOC_Os11g26000.1 upstream_gene_variant ; 533.0bp to feature; MODIFIER silent_mutation Average:9.812; most accessible tissue: Callus, score: 42.522 N N N N
vg1114869295 T -> C LOC_Os11g25990-LOC_Os11g26000 intergenic_region ; MODIFIER silent_mutation Average:9.812; most accessible tissue: Callus, score: 42.522 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114869295 4.77E-08 NA mr1079 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
vg1114869295 NA 4.76E-09 mr1198 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
vg1114869295 NA 1.76E-08 mr1302 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
vg1114869295 NA 2.26E-06 mr1315 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
vg1114869295 NA 2.55E-14 mr1376 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
vg1114869295 6.88E-07 NA mr1390 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
vg1114869295 NA 2.55E-14 mr1431 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
vg1114869295 2.48E-06 NA mr1490 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
vg1114869295 9.96E-06 9.30E-90 mr1758 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
vg1114869295 NA 9.47E-11 mr1775 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
vg1114869295 NA 8.55E-07 mr1886 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
vg1114869295 NA 1.99E-07 mr1821_2 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