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Detailed information for vg1200937807:

Variant ID: vg1200937807 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 937807
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GATTTTGAGTTTTTACTTGCACTGTTTGACCACTTGTCCTATTCAAAAAAATTTGGAATTATTATTTAATTTTTTTGTGACACTTTATTATCCAAAGTAC[T/A]
TTAAGCACAACTTTTTGTTTTTTGTATTTGCACAAATTTTATAAATAAGACGAGTGGTCAAACAGTGCAAGTAAAAGCCCAAAATCCCTTATATTATAGG

Reverse complement sequence

CCTATAATATAAGGGATTTTGGGCTTTTACTTGCACTGTTTGACCACTCGTCTTATTTATAAAATTTGTGCAAATACAAAAAACAAAAAGTTGTGCTTAA[A/T]
GTACTTTGGATAATAAAGTGTCACAAAAAAATTAAATAATAATTCCAAATTTTTTTGAATAGGACAAGTGGTCAAACAGTGCAAGTAAAAACTCAAAATC

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 92.40% 7.40% 0.17% 0.00% NA
All Indica  2759 87.20% 12.60% 0.25% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.80% 21.70% 0.50% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 91.70% 8.20% 0.11% 0.00% NA
Indica Intermediate  786 84.00% 15.60% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 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 96.70% 2.20% 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
vg1200937807 T -> A LOC_Os12g02690.1 upstream_gene_variant ; 3051.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02690.3 upstream_gene_variant ; 3045.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02690.2 upstream_gene_variant ; 3051.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02690.4 upstream_gene_variant ; 3059.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02670.1 downstream_gene_variant ; 3278.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02680.1 downstream_gene_variant ; 385.0bp to feature; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg1200937807 T -> A LOC_Os12g02680-LOC_Os12g02690 intergenic_region ; MODIFIER silent_mutation Average:56.632; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200937807 NA 2.46E-06 mr1007 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
vg1200937807 3.87E-06 6.61E-07 mr1231 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