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Detailed information for vg0216301746:

Variant ID: vg0216301746 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16301746
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCCAGTATGTACTATGCTACTAACATATATGCAGGAGAAGCACACATAAATGGAGGAGAATTGACGGAACATAAACAAACAATTAACTGGAAGCTGTC[G/A]
AAAGGTATACTCATGAATGGTTGGGTCTCTAAACCCAGTAAAATAATATCAATTGGGCTCAACCATTACAACTACTAGGCTGAGGAATCAACGAGGAGTA

Reverse complement sequence

TACTCCTCGTTGATTCCTCAGCCTAGTAGTTGTAATGGTTGAGCCCAATTGATATTATTTTACTGGGTTTAGAGACCCAACCATTCATGAGTATACCTTT[C/T]
GACAGCTTCCAGTTAATTGTTTGTTTATGTTCCGTCAATTCTCCTCCATTTATGTGTGCTTCTCCTGCATATATGTTAGTAGCATAGTACATACTGGAAG

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 97.80% 1.40% 0.76% 0.00% NA
All Indica  2759 96.40% 2.40% 1.23% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 90.10% 5.70% 4.20% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 1.10% 1.15% 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  241 100.00% 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
vg0216301746 G -> A LOC_Os02g27520-LOC_Os02g27540 intergenic_region ; MODIFIER silent_mutation Average:64.056; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216301746 NA 7.74E-08 mr1559 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