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Detailed information for vg0229359655:

Variant ID: vg0229359655 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29359655
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTAATGTTTTAATTTTATTAATAGACCATTTCTAAAAGTATTTTCAAGAAATGAATCTTTCTTTTGGTGCCCAAATAACTCTCACGCCACACGCAGCC[G/A]
GTGTCTGCCACGCACTGTAGCTGGCATGGCCAAACCACCCTGCCACTGCCAGGCAGGCGTGGCCAAAAGGTTTATTTCTTAAAAATACTTTTAGAAAGTC

Reverse complement sequence

GACTTTCTAAAAGTATTTTTAAGAAATAAACCTTTTGGCCACGCCTGCCTGGCAGTGGCAGGGTGGTTTGGCCATGCCAGCTACAGTGCGTGGCAGACAC[C/T]
GGCTGCGTGTGGCGTGAGAGTTATTTGGGCACCAAAAGAAAGATTCATTTCTTGAAAATACTTTTAGAAATGGTCTATTAATAAAATTAAAACATTAAAA

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 81.90% 18.00% 0.11% 0.00% NA
All Indica  2759 69.60% 30.20% 0.18% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.20% 19.50% 0.34% 0.00% NA
Indica II  465 56.60% 43.20% 0.22% 0.00% NA
Indica III  913 63.70% 36.10% 0.11% 0.00% NA
Indica Intermediate  786 76.10% 23.80% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0229359655 G -> A LOC_Os02g47980.1 upstream_gene_variant ; 4432.0bp to feature; MODIFIER silent_mutation Average:58.979; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0229359655 G -> A LOC_Os02g47970.1 downstream_gene_variant ; 1764.0bp to feature; MODIFIER silent_mutation Average:58.979; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0229359655 G -> A LOC_Os02g47970-LOC_Os02g47980 intergenic_region ; MODIFIER silent_mutation Average:58.979; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229359655 3.72E-07 NA mr1156_2 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
vg0229359655 2.66E-06 8.98E-07 mr1156_2 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
vg0229359655 NA 1.13E-06 mr1974_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
vg0229359655 NA 6.79E-06 mr1974_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