Search for Variation information by Variation ID:

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

Detailed information for vg0220790529:

Variant ID: vg0220790529 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20790529
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AGCATTTCTCTTTTGGAGCGTTCTGGAAATTTTCGGAAGTTCCGAAAAGAATTTTTAGAAGTTCCGAAAATACACAGAACCGTGTTTGAGCGTTCTGGAA[A/T]
TTTTCGGAAGTTCCGAAAATACACAGAACCGTTTGAGAGCTCTCTGGAAATTTTCGGAAGTTCCGAAAATACACAGAAGCGTTCTGGAAATTTTCGGAAG

Reverse complement sequence

CTTCCGAAAATTTCCAGAACGCTTCTGTGTATTTTCGGAACTTCCGAAAATTTCCAGAGAGCTCTCAAACGGTTCTGTGTATTTTCGGAACTTCCGAAAA[T/A]
TTCCAGAACGCTCAAACACGGTTCTGTGTATTTTCGGAACTTCTAAAAATTCTTTTCGGAACTTCCGAAAATTTCCAGAACGCTCCAAAAGAGAAATGCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 0.90% 1.99% 0.00% NA
All Indica  2759 97.00% 0.70% 2.32% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 82.90% 6.70% 10.41% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 88.80% 2.20% 9.03% 0.00% NA
Indica III  913 97.70% 0.80% 1.53% 0.00% NA
Indica Intermediate  786 98.60% 0.40% 1.02% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg0220790529 A -> T LOC_Os02g34650.1 upstream_gene_variant ; 4576.0bp to feature; MODIFIER silent_mutation Average:25.416; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N
vg0220790529 A -> T LOC_Os02g34660.1 upstream_gene_variant ; 1037.0bp to feature; MODIFIER silent_mutation Average:25.416; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N
vg0220790529 A -> T LOC_Os02g34670.1 upstream_gene_variant ; 4898.0bp to feature; MODIFIER silent_mutation Average:25.416; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N
vg0220790529 A -> T LOC_Os02g34650-LOC_Os02g34660 intergenic_region ; MODIFIER silent_mutation Average:25.416; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220790529 NA 1.77E-06 mr1113 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
vg0220790529 7.11E-06 6.14E-08 mr1114 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