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Detailed information for vg1002252247:

Variant ID: vg1002252247 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2252247
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, T: 0.26, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGCCGCCGTTGCCGCAGAGCTGCGCCAGTAGTTCGCCGGCGGCGAGCGGCATGATGCTAAGGAGGAGCAGGACGCCGACCATGGCGAACGACGGTTT[A/T]
CCTGTAGTTGCATGCTTGGTGTTTTATCCGGAATCAACCTGTAGAGATTTTTTTTTTCAAAAAAGAAATAAATAAAATGGTAATGAAACAATACTCCCAG

Reverse complement sequence

CTGGGAGTATTGTTTCATTACCATTTTATTTATTTCTTTTTTGAAAAAAAAAATCTCTACAGGTTGATTCCGGATAAAACACCAAGCATGCAACTACAGG[T/A]
AAACCGTCGTTCGCCATGGTCGGCGTCCTGCTCCTCCTTAGCATCATGCCGCTCGCCGCCGGCGAACTACTGGCGCAGCTCTGCGGCAACGGCGGCAACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.60% 38.40% 0.00% 0.00% NA
All Indica  2759 83.50% 16.50% 0.00% 0.00% NA
All Japonica  1512 15.90% 84.10% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 0.00% 0.00% NA
Indica I  595 67.10% 32.90% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 82.80% 17.20% 0.00% 0.00% NA
Indica Intermediate  786 89.20% 10.80% 0.00% 0.00% NA
Temperate Japonica  767 8.90% 91.10% 0.00% 0.00% NA
Tropical Japonica  504 22.20% 77.80% 0.00% 0.00% NA
Japonica Intermediate  241 25.30% 74.70% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg1002252247 A -> T LOC_Os10g04720.1 upstream_gene_variant ; 16.0bp to feature; MODIFIER silent_mutation Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N
vg1002252247 A -> T LOC_Os10g04710.1 downstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N
vg1002252247 A -> T LOC_Os10g04720-LOC_Os10g04730 intergenic_region ; MODIFIER silent_mutation Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002252247 2.15E-08 NA mr1486 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
vg1002252247 1.90E-08 3.25E-24 mr1548 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
vg1002252247 NA 1.32E-19 mr1588 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
vg1002252247 NA 1.13E-06 mr1709 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
vg1002252247 3.06E-07 NA mr1486_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
vg1002252247 NA 1.94E-11 mr1709_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