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Detailed information for vg0915924541:

Variant ID: vg0915924541 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15924541
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, G: 0.20, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGATGACGTTATTGACTTTTTCTCACATGTTTGACCATTCGTCTTATTCAAAATTTTTATGCAAATGTATAAGATATAAATCACATTTAAAATACTAT[A/G]
AGTGATAAAACAACTCATAACAAAATAAATTATAATTACGTAAATTTTTTGAATAAGACAAATAGTCAAATATGTGAGAAAAAGTTAACGGCGTCATCTA

Reverse complement sequence

TAGATGACGCCGTTAACTTTTTCTCACATATTTGACTATTTGTCTTATTCAAAAAATTTACGTAATTATAATTTATTTTGTTATGAGTTGTTTTATCACT[T/C]
ATAGTATTTTAAATGTGATTTATATCTTATACATTTGCATAAAAATTTTGAATAAGACGAATGGTCAAACATGTGAGAAAAAGTCAATAACGTCATCTAT

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 85.10% 14.90% 0.00% 0.00% NA
All Indica  2759 77.10% 22.90% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 79.90% 20.10% 0.00% 0.00% NA
Indica I  595 89.90% 10.10% 0.00% 0.00% NA
Indica II  465 45.20% 54.80% 0.00% 0.00% NA
Indica III  913 83.40% 16.60% 0.00% 0.00% NA
Indica Intermediate  786 79.00% 21.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0915924541 A -> G LOC_Os09g26360.1 upstream_gene_variant ; 471.0bp to feature; MODIFIER silent_mutation Average:58.388; most accessible tissue: Callus, score: 81.176 N N N N
vg0915924541 A -> G LOC_Os09g26370.1 upstream_gene_variant ; 2484.0bp to feature; MODIFIER silent_mutation Average:58.388; most accessible tissue: Callus, score: 81.176 N N N N
vg0915924541 A -> G LOC_Os09g26360-LOC_Os09g26370 intergenic_region ; MODIFIER silent_mutation Average:58.388; most accessible tissue: Callus, score: 81.176 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915924541 NA 4.77E-06 mr1044 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
vg0915924541 NA 1.52E-06 mr1319 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
vg0915924541 NA 4.98E-08 mr1482 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
vg0915924541 NA 1.47E-09 mr1565 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