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Detailed information for vg0110090809:

Variant ID: vg0110090809 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 10090809
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GCGGAGGACACAGAGATTTTATACTGGTTCGGGCCTCCATGGTGGATAATAGCCCTATATCCATTTTTTTTTCTTGCCGAAAGGCTTTCATAGTGCCGAA[G/A]
GGCTTCCATGATAGTATGTATATTTTTACAATTTGGCGATTTGGGTGCCACCCATTCTAGACATAGAAGCGCTTGAGAGAGGCGGCGTTCCAGGAATGGT

Reverse complement sequence

ACCATTCCTGGAACGCCGCCTCTCTCAAGCGCTTCTATGTCTAGAATGGGTGGCACCCAAATCGCCAAATTGTAAAAATATACATACTATCATGGAAGCC[C/T]
TTCGGCACTATGAAAGCCTTTCGGCAAGAAAAAAAAATGGATATAGGGCTATTATCCACCATGGAGGCCCGAACCAGTATAAAATCTCTGTGTCCTCCGC

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 43.50% 29.70% 12.10% 14.71% NA
All Indica  2759 12.30% 46.60% 19.06% 22.00% NA
All Japonica  1512 96.80% 2.20% 0.66% 0.40% NA
Aus  269 71.70% 3.70% 1.49% 23.05% NA
Indica I  595 7.60% 48.60% 23.87% 20.00% NA
Indica II  465 16.80% 43.70% 18.49% 21.08% NA
Indica III  913 11.40% 47.60% 16.76% 24.21% NA
Indica Intermediate  786 14.20% 45.80% 18.45% 21.50% NA
Temperate Japonica  767 98.30% 1.00% 0.39% 0.26% NA
Tropical Japonica  504 94.60% 3.80% 1.19% 0.40% NA
Japonica Intermediate  241 96.30% 2.50% 0.41% 0.83% NA
VI/Aromatic  96 16.70% 54.20% 16.67% 12.50% NA
Intermediate  90 51.10% 22.20% 17.78% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0110090809 G -> A LOC_Os01g18030.1 downstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:29.198; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0110090809 G -> A LOC_Os01g18040.1 downstream_gene_variant ; 57.0bp to feature; MODIFIER silent_mutation Average:29.198; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0110090809 G -> A LOC_Os01g18030-LOC_Os01g18040 intergenic_region ; MODIFIER silent_mutation Average:29.198; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0110090809 G -> DEL N N silent_mutation Average:29.198; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0110090809 1.74E-06 NA mr1069 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
vg0110090809 2.90E-06 NA mr1069 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
vg0110090809 7.04E-06 7.04E-06 mr1355 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
vg0110090809 2.91E-06 NA mr1671 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