Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0205646080:

Variant ID: vg0205646080 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5646080
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCCGCGGCTTTCTTTTTTTTTTTGATCCCGTGCACCAGAAAGGAGAGAAAAGCCACCTTTTTAAGTGGGCCACACCCAAAATAGCTCCAATTAGCACC[C/T]
CTTAAGTGGGATAGTTTTTTGGGGTGGGTTATTTCCAAATAGTTCTCAAATAGCTCACCATTTTGGATCTTTTGGGCTATTTTAGCCATTTGAGGGAGGG

Reverse complement sequence

CCCTCCCTCAAATGGCTAAAATAGCCCAAAAGATCCAAAATGGTGAGCTATTTGAGAACTATTTGGAAATAACCCACCCCAAAAAACTATCCCACTTAAG[G/A]
GGTGCTAATTGGAGCTATTTTGGGTGTGGCCCACTTAAAAAGGTGGCTTTTCTCTCCTTTCTGGTGCACGGGATCAAAAAAAAAAAGAAAGCCGCGGCTC

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 51.40% 48.40% 0.19% 0.00% NA
All Indica  2759 29.40% 70.30% 0.33% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 20.40% 79.60% 0.00% 0.00% NA
Indica I  595 30.40% 69.40% 0.17% 0.00% NA
Indica II  465 30.10% 69.70% 0.22% 0.00% NA
Indica III  913 27.10% 72.50% 0.44% 0.00% NA
Indica Intermediate  786 30.90% 68.70% 0.38% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0205646080 C -> T LOC_Os02g10720.1 upstream_gene_variant ; 1450.0bp to feature; MODIFIER silent_mutation Average:64.452; most accessible tissue: Zhenshan97 flag leaf, score: 76.061 N N N N
vg0205646080 C -> T LOC_Os02g10720-LOC_Os02g10730 intergenic_region ; MODIFIER silent_mutation Average:64.452; most accessible tissue: Zhenshan97 flag leaf, score: 76.061 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205646080 3.93E-06 NA mr1007 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
vg0205646080 1.17E-06 1.17E-06 mr1575 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
vg0205646080 NA 3.89E-09 mr1746 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
vg0205646080 NA 3.03E-10 mr1170_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
vg0205646080 NA 1.04E-10 mr1705_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
vg0205646080 NA 5.00E-06 mr1705_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