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Detailed information for vg0507480268:

Variant ID: vg0507480268 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7480268
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAAGTAATTATTAATTATTTTCCTATCATTTAATTCATGGTTAAATATACTTTCATGTATATATATTTTACAAAAACTTTTTTTATAAGACGAATGAT[C/T]
AAATATGTTTAAAAGAGTGAACAACGTTAAATATTCGAGGAGAGAGAGAATATCTAATAAGGCGTGGTGGTGCTTGGCAGTTGCATAGCAACAGGACGGA

Reverse complement sequence

TCCGTCCTGTTGCTATGCAACTGCCAAGCACCACCACGCCTTATTAGATATTCTCTCTCTCCTCGAATATTTAACGTTGTTCACTCTTTTAAACATATTT[G/A]
ATCATTCGTCTTATAAAAAAAGTTTTTGTAAAATATATATACATGAAAGTATATTTAACCATGAATTAAATGATAGGAAAATAATTAATAATTACTTAAA

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 97.90% 1.10% 1.02% 0.00% NA
All Indica  2759 99.80% 0.00% 0.22% 0.00% NA
All Japonica  1512 93.70% 3.50% 2.78% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.00% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 90.60% 5.10% 4.30% 0.00% NA
Tropical Japonica  504 99.20% 0.00% 0.79% 0.00% NA
Japonica Intermediate  241 92.10% 5.80% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0507480268 C -> T LOC_Os05g13470.1 upstream_gene_variant ; 4570.0bp to feature; MODIFIER silent_mutation Average:81.058; most accessible tissue: Callus, score: 93.158 N N N N
vg0507480268 C -> T LOC_Os05g13490.1 upstream_gene_variant ; 917.0bp to feature; MODIFIER silent_mutation Average:81.058; most accessible tissue: Callus, score: 93.158 N N N N
vg0507480268 C -> T LOC_Os05g13500.1 upstream_gene_variant ; 1667.0bp to feature; MODIFIER silent_mutation Average:81.058; most accessible tissue: Callus, score: 93.158 N N N N
vg0507480268 C -> T LOC_Os05g13480.1 downstream_gene_variant ; 3228.0bp to feature; MODIFIER silent_mutation Average:81.058; most accessible tissue: Callus, score: 93.158 N N N N
vg0507480268 C -> T LOC_Os05g13490-LOC_Os05g13500 intergenic_region ; MODIFIER silent_mutation Average:81.058; most accessible tissue: Callus, score: 93.158 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507480268 NA 5.55E-06 Grain_weight Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507480268 5.33E-09 5.33E-09 mr1024_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
vg0507480268 NA 8.87E-07 mr1092_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
vg0507480268 NA 2.99E-07 mr1097_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
vg0507480268 NA 2.36E-06 mr1152_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
vg0507480268 1.02E-06 1.02E-06 mr1317_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
vg0507480268 3.98E-10 2.06E-11 mr1565_2 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
vg0507480268 NA 8.18E-06 mr1827_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
vg0507480268 2.02E-06 2.02E-06 mr1897_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
vg0507480268 8.93E-07 8.92E-07 mr1914_2 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
vg0507480268 2.43E-06 2.43E-06 mr1915_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
vg0507480268 NA 3.06E-06 mr1922_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
vg0507480268 1.83E-07 1.83E-07 mr1940_2 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