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Detailed information for vg0512797069:

Variant ID: vg0512797069 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 12797069
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GACCAATCATCTCACCGATAACGATTTTGCCGTCTAAAAGAAATAACAGTAACGATAAATGCCAAAACATGTAAAAATCTAAAATGATGTAAAATGCATG[A/G]
GTTTACTAGTGTGGTTAGGTACTCTTCTAAGATGAAATTAGGTGAAAGAATTTATATTTTATCACTTTGCATTAGAGAGTTATAAATTTTCAAAGTTTAA

Reverse complement sequence

TTAAACTTTGAAAATTTATAACTCTCTAATGCAAAGTGATAAAATATAAATTCTTTCACCTAATTTCATCTTAGAAGAGTACCTAACCACACTAGTAAAC[T/C]
CATGCATTTTACATCATTTTAGATTTTTACATGTTTTGGCATTTATCGTTACTGTTATTTCTTTTAGACGGCAAAATCGTTATCGGTGAGATGATTGGTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 0.40% 0.61% 0.00% NA
All Indica  2759 99.80% 0.00% 0.22% 0.00% NA
All Japonica  1512 97.50% 1.00% 1.52% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.00% 0.84% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.70% 2.00% 2.35% 0.00% NA
Tropical Japonica  504 99.00% 0.00% 0.99% 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 97.80% 2.20% 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
vg0512797069 A -> G LOC_Os05g22530.1 downstream_gene_variant ; 2223.0bp to feature; MODIFIER silent_mutation Average:41.72; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N
vg0512797069 A -> G LOC_Os05g22540.1 downstream_gene_variant ; 2337.0bp to feature; MODIFIER silent_mutation Average:41.72; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N
vg0512797069 A -> G LOC_Os05g22530-LOC_Os05g22540 intergenic_region ; MODIFIER silent_mutation Average:41.72; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0512797069 1.50E-07 1.50E-07 mr1173_2 Jap_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
vg0512797069 4.37E-06 1.13E-06 mr1546_2 Jap_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