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Detailed information for vg0412128903:

Variant ID: vg0412128903 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12128903
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCCGCCAACGGCGCCAGAATTGCTTGTTGGTATTTCTTAACGGCATTACAAGAAATATAATTCCCAACAATGGCGCAGAAATATTTCTGGTATATTAT[G/T]
GTTACAGAGTTCATCCGCAAGCGCATGGATATACCATTGTAGCATTTCACCTTAGAGTATTCCAATGGTATCGTATTTATTTTATCCCGTGGGAAGATCA

Reverse complement sequence

TGATCTTCCCACGGGATAAAATAAATACGATACCATTGGAATACTCTAAGGTGAAATGCTACAATGGTATATCCATGCGCTTGCGGATGAACTCTGTAAC[C/A]
ATAATATACCAGAAATATTTCTGCGCCATTGTTGGGAATTATATTTCTTGTAATGCCGTTAAGAAATACCAACAAGCAATTCTGGCGCCGTTGGCGGGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.60% 41.50% 0.89% 0.00% NA
All Indica  2759 92.10% 6.50% 1.41% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 48.00% 51.70% 0.37% 0.00% NA
Indica I  595 98.80% 0.80% 0.34% 0.00% NA
Indica II  465 94.40% 4.70% 0.86% 0.00% NA
Indica III  913 86.60% 10.50% 2.85% 0.00% NA
Indica Intermediate  786 91.90% 7.30% 0.89% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 41.10% 56.70% 2.22% 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
vg0412128903 G -> T LOC_Os04g21450.1 upstream_gene_variant ; 580.0bp to feature; MODIFIER silent_mutation Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0412128903 G -> T LOC_Os04g21450-LOC_Os04g21460 intergenic_region ; MODIFIER silent_mutation Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412128903 1.07E-06 1.54E-07 mr1071 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
vg0412128903 NA 2.75E-06 mr1080 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
vg0412128903 NA 8.06E-06 mr1140 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
vg0412128903 NA 4.01E-16 mr1156 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
vg0412128903 NA 8.26E-16 mr1700 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
vg0412128903 NA 2.46E-53 mr1795 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
vg0412128903 NA 1.15E-07 mr1804_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