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Detailed information for vg0225551985:

Variant ID: vg0225551985 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25551985
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGGCTTAACAGATTCATCTCGCTACTTAAGATTAAGATCTTTATGTGGTACTTACTTAAAGGGGTGGTGCTAACTAAGGACAATTTGGCAAGACGGAA[C/T]
TGGAATGGCAGTTTAAGATGTTGTTTCTGTATAAAAAATGAGACCATTCAACATCTTTTTCTTGACTGTCATTATGCAAAATTTGTTTGGAGAATAGTAC

Reverse complement sequence

GTACTATTCTCCAAACAAATTTTGCATAATGACAGTCAAGAAAAAGATGTTGAATGGTCTCATTTTTTATACAGAAACAACATCTTAAACTGCCATTCCA[G/A]
TTCCGTCTTGCCAAATTGTCCTTAGTTAGCACCACCCCTTTAAGTAAGTACCACATAAAGATCTTAATCTTAAGTAGCGAGATGAATCTGTTAAGCCTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.00% 34.80% 0.13% 0.00% NA
All Indica  2759 97.40% 2.60% 0.07% 0.00% NA
All Japonica  1512 5.20% 94.60% 0.20% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 5.00% 0.25% 0.00% NA
Temperate Japonica  767 1.00% 98.60% 0.39% 0.00% NA
Tropical Japonica  504 13.30% 86.70% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 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
vg0225551985 C -> T LOC_Os02g42470.1 upstream_gene_variant ; 1167.0bp to feature; MODIFIER silent_mutation Average:44.49; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0225551985 C -> T LOC_Os02g42460.1 downstream_gene_variant ; 4576.0bp to feature; MODIFIER silent_mutation Average:44.49; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0225551985 C -> T LOC_Os02g42470-LOC_Os02g42497 intergenic_region ; MODIFIER silent_mutation Average:44.49; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225551985 NA 4.33E-12 mr1170 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
vg0225551985 NA 1.77E-10 mr1175 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
vg0225551985 2.86E-07 2.21E-81 mr1629 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