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Detailed information for vg0224824813:

Variant ID: vg0224824813 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24824813
Reference Allele: TAlternative Allele: G,A
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, T: 0.26, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


CTACTACGAGCACACCACATTAAGTCTTCGCATTTGGGAATAGAGATATGGGTGGAGGTGGAGGCTCGAAGGGAGGCCATGAGGGCAGGATCCTAGAAAA[T/G,A]
GAGGGAGATGGTGGTAAGACAATGGATAGCGCCACATTAAGTCTCTGCATTTGGGAATAGAGATATTGGTGGAGGTGGAGGTGGAGGCTCGAAGGGAGGC

Reverse complement sequence

GCCTCCCTTCGAGCCTCCACCTCCACCTCCACCAATATCTCTATTCCCAAATGCAGAGACTTAATGTGGCGCTATCCATTGTCTTACCACCATCTCCCTC[A/C,T]
TTTTCTAGGATCCTGCCCTCATGGCCTCCCTTCGAGCCTCCACCTCCACCCATATCTCTATTCCCAAATGCGAAGACTTAATGTGGTGTGCTCGTAGTAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.80% 14.30% 0.55% 0.21% A: 0.15%
All Indica  2759 83.00% 15.60% 0.76% 0.36% A: 0.25%
All Japonica  1512 91.90% 7.80% 0.26% 0.00% NA
Aus  269 87.40% 12.30% 0.37% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 82.60% 17.40% 0.00% 0.00% NA
Indica III  913 71.60% 25.20% 1.53% 0.88% A: 0.77%
Indica Intermediate  786 84.70% 14.10% 0.89% 0.25% NA
Temperate Japonica  767 91.40% 8.20% 0.39% 0.00% NA
Tropical Japonica  504 92.10% 7.90% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.41% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0224824813 T -> A LOC_Os02g41450.1 downstream_gene_variant ; 4995.0bp to feature; MODIFIER silent_mutation Average:68.234; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0224824813 T -> A LOC_Os02g41450-LOC_Os02g41460 intergenic_region ; MODIFIER silent_mutation Average:68.234; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0224824813 T -> G LOC_Os02g41450.1 downstream_gene_variant ; 4995.0bp to feature; MODIFIER silent_mutation Average:68.234; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0224824813 T -> G LOC_Os02g41450-LOC_Os02g41460 intergenic_region ; MODIFIER silent_mutation Average:68.234; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0224824813 T -> DEL N N silent_mutation Average:68.234; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224824813 6.21E-06 NA mr1098 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
vg0224824813 3.49E-07 NA mr1101 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
vg0224824813 3.80E-06 NA mr1868 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
vg0224824813 4.43E-06 NA mr1095_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
vg0224824813 5.08E-07 NA mr1098_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
vg0224824813 5.74E-06 NA mr1099_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
vg0224824813 6.70E-09 6.36E-06 mr1099_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
vg0224824813 3.62E-06 NA mr1120_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
vg0224824813 1.78E-06 NA mr1123_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
vg0224824813 9.72E-06 NA mr1146_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
vg0224824813 2.64E-09 NA mr1150_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
vg0224824813 6.93E-06 NA mr1222_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
vg0224824813 8.01E-06 NA mr1247_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