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Detailed information for vg0404403925:

Variant ID: vg0404403925 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4403925
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGGGAACCTGGACAAACGAACTGAGCCTTAGAAGCAGTAGCGGCATGCACGACGATGGATAGAAAAGGAGAGGAGGGATCTAGCCACACTGCTTGGAT[C/T]
TGCTCGTGAGCACCGAAGCTCGTTGCTCACGCCCTCCTCGGGAGTTGCCATGGCATGGGAAAGAGAGGATGTCCACGGCGACGATGACGACGAAGCAGCG

Reverse complement sequence

CGCTGCTTCGTCGTCATCGTCGCCGTGGACATCCTCTCTTTCCCATGCCATGGCAACTCCCGAGGAGGGCGTGAGCAACGAGCTTCGGTGCTCACGAGCA[G/A]
ATCCAAGCAGTGTGGCTAGATCCCTCCTCTCCTTTTCTATCCATCGTCGTGCATGCCGCTACTGCTTCTAAGGCTCAGTTCGTTTGTCCAGGTTCCCAAC

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 85.10% 14.80% 0.13% 0.00% NA
All Indica  2759 75.50% 24.30% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 98.70% 1.20% 0.17% 0.00% NA
Indica II  465 76.60% 23.20% 0.22% 0.00% NA
Indica III  913 56.70% 43.00% 0.22% 0.00% NA
Indica Intermediate  786 79.10% 20.60% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0404403925 C -> T LOC_Os04g08250.1 upstream_gene_variant ; 1045.0bp to feature; MODIFIER silent_mutation Average:66.226; most accessible tissue: Callus, score: 88.801 N N N N
vg0404403925 C -> T LOC_Os04g08260.1 upstream_gene_variant ; 217.0bp to feature; MODIFIER silent_mutation Average:66.226; most accessible tissue: Callus, score: 88.801 N N N N
vg0404403925 C -> T LOC_Os04g08250-LOC_Os04g08260 intergenic_region ; MODIFIER silent_mutation Average:66.226; most accessible tissue: Callus, score: 88.801 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404403925 1.58E-06 NA mr1167_2 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
vg0404403925 3.20E-06 NA mr1167_2 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
vg0404403925 9.04E-06 NA mr1726_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
vg0404403925 1.74E-06 2.22E-06 mr1726_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
vg0404403925 4.46E-06 NA mr1950_2 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
vg0404403925 2.60E-06 1.30E-06 mr1950_2 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