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Detailed information for vg0134213880:

Variant ID: vg0134213880 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34213880
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGATTTTCAAAAATAAACAAAATGAGGATGGTTTGATTGTGAGAAATAAAGCTAGACTTGTTGCTCAAGGTTTTACTCAAGTTGAGGGTTTGGATTTT[G/A]
ATGAAACTTTTGCTCATGTTGCTAGAATTGAGGCAATTAGACTTTTGTTGGCTTTTGCTGCTTCAAAAGGATTTAAATTGTATCAAATGGATGTGAAAAG

Reverse complement sequence

CTTTTCACATCCATTTGATACAATTTAAATCCTTTTGAAGCAGCAAAAGCCAACAAAAGTCTAATTGCCTCAATTCTAGCAACATGAGCAAAAGTTTCAT[C/T]
AAAATCCAAACCCTCAACTTGAGTAAAACCTTGAGCAACAAGTCTAGCTTTATTTCTCACAATCAAACCATCCTCATTTTGTTTATTTTTGAAAATCCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.10% 37.10% 1.80% 0.00% NA
All Indica  2759 39.00% 58.10% 2.86% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 48.70% 49.40% 1.86% 0.00% NA
Indica I  595 25.20% 69.90% 4.87% 0.00% NA
Indica II  465 75.50% 23.70% 0.86% 0.00% NA
Indica III  913 24.50% 72.70% 2.74% 0.00% NA
Indica Intermediate  786 44.70% 52.70% 2.67% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 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
vg0134213880 G -> A LOC_Os01g59220.1 missense_variant ; p.Asp650Asn; MODERATE nonsynonymous_codon ; D650N Average:12.842; most accessible tissue: Zhenshan97 flag leaf, score: 22.512 benign 0.442 TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134213880 3.52E-06 NA mr1786 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
vg0134213880 5.90E-06 5.90E-06 mr1786 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