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Detailed information for vg0229569578:

Variant ID: vg0229569578 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29569578
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GTATCGTACATGCACTTCCGGAGGTTGAAGACGATAGGGCTGAAAAGGAAGAAAATAATGGGCTTTCGGTCCAAAACCAAATAAGGAGTATAATGTATAG[G/A]
CGATAAAAAATATTTTTACCCATTGCAACGCATGGGCATTTTTTCTAGTAAAAGAAAAGAGACTAGCTTCAGCAACCATGAAATCCCAAGCTAGTTCTTA

Reverse complement sequence

TAAGAACTAGCTTGGGATTTCATGGTTGCTGAAGCTAGTCTCTTTTCTTTTACTAGAAAAAATGCCCATGCGTTGCAATGGGTAAAAATATTTTTTATCG[C/T]
CTATACATTATACTCCTTATTTGGTTTTGGACCGAAAGCCCATTATTTTCTTCCTTTTCAGCCCTATCGTCTTCAACCTCCGGAAGTGCATGTACGATAC

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 98.30% 1.70% 0.00% 0.00% NA
All Indica  2759 97.10% 2.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 86.90% 13.10% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 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  90 100.00% 0.00% 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
vg0229569578 G -> A LOC_Os02g48320.1 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:42.834; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0229569578 G -> A LOC_Os02g48320.3 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:42.834; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0229569578 G -> A LOC_Os02g48320.2 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:42.834; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0229569578 G -> A LOC_Os02g48300-LOC_Os02g48320 intergenic_region ; MODIFIER silent_mutation Average:42.834; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229569578 NA 6.17E-06 mr1088 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
vg0229569578 NA 2.58E-06 mr1122 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
vg0229569578 NA 3.13E-07 mr1169 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
vg0229569578 NA 1.44E-18 mr1498 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
vg0229569578 NA 2.43E-06 mr1629 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
vg0229569578 NA 1.66E-15 mr1769 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
vg0229569578 NA 2.09E-08 mr1903 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
vg0229569578 NA 4.16E-10 mr1925 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
vg0229569578 NA 9.26E-14 mr1951 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
vg0229569578 NA 3.76E-06 mr1188_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
vg0229569578 NA 1.20E-08 mr1310_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
vg0229569578 NA 1.70E-06 mr1322_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
vg0229569578 NA 3.45E-15 mr1498_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
vg0229569578 NA 3.35E-15 mr1769_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
vg0229569578 NA 1.63E-09 mr1925_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
vg0229569578 NA 3.34E-12 mr1951_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