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Detailed information for vg0123166741:

Variant ID: vg0123166741 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23166741
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTAGATCAATTTGGAATGGAGGGAATATGTTTTTTATTAAAAAAATTTCTATGGAAAAGTTGTTTGAAAAATCATATTAATTTATTTTTAATTTTTTTA[G/T]
CTAATATTTAATCAATCATGATATAACGAGTCATTCTGTTTTTCGTGTGGAAAGTATAAGTTCCCAACACATGTACAATAGAACACAGCCCTAAGCCTAA

Reverse complement sequence

TTAGGCTTAGGGCTGTGTTCTATTGTACATGTGTTGGGAACTTATACTTTCCACACGAAAAACAGAATGACTCGTTATATCATGATTGATTAAATATTAG[C/A]
TAAAAAAATTAAAAATAAATTAATATGATTTTTCAAACAACTTTTCCATAGAAATTTTTTTAATAAAAAACATATTCCCTCCATTCCAAATTGATCTACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 3.10% 0.08% 0.00% NA
All Indica  2759 99.70% 0.30% 0.04% 0.00% NA
All Japonica  1512 91.00% 8.80% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 76.00% 23.60% 0.40% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 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
vg0123166741 G -> T LOC_Os01g40940.1 upstream_gene_variant ; 3247.0bp to feature; MODIFIER silent_mutation Average:34.843; most accessible tissue: Callus, score: 63.135 N N N N
vg0123166741 G -> T LOC_Os01g40960.1 upstream_gene_variant ; 4522.0bp to feature; MODIFIER silent_mutation Average:34.843; most accessible tissue: Callus, score: 63.135 N N N N
vg0123166741 G -> T LOC_Os01g40950.1 downstream_gene_variant ; 865.0bp to feature; MODIFIER silent_mutation Average:34.843; most accessible tissue: Callus, score: 63.135 N N N N
vg0123166741 G -> T LOC_Os01g40940-LOC_Os01g40950 intergenic_region ; MODIFIER silent_mutation Average:34.843; most accessible tissue: Callus, score: 63.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123166741 NA 9.02E-06 mr1076 Jap_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
vg0123166741 NA 7.76E-06 mr1083 Jap_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
vg0123166741 1.20E-07 5.75E-07 mr1226 Jap_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
vg0123166741 2.05E-07 NA mr1411 Jap_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
vg0123166741 3.51E-06 3.51E-06 mr1076_2 Jap_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
vg0123166741 4.91E-06 1.83E-07 mr1082_2 Jap_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
vg0123166741 NA 9.64E-06 mr1083_2 Jap_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