Exact(33)
All SNPs, except rs302678, were polymorphic.
All SNPs except rs736118 (STrs974456974456 (STRand and rs5418 (GLUT4) were genotyped by Tetraprimer ARMS PCR.
Pairwise linkage disequilibrium (LD) measure D' was 1.00 between all SNPs except between rs10838524 and rs7123390 where D' was 0.67.
Data on the prevalence of the fast acetylation phenotype were considered only for the samples genotyped for all four slow-causing variants, to which we added the non-African samples genotyped for all SNPs except 191G>A (See Table S1).
The observed allele frequencies for all SNPs, except for 5237A>G among women (p = 0.03) and 4741G>C among men (p = 0.001), were within Hardy-Weinberg equilibrium among the controls.
As the SNP 191G>A has been shown to be rare in non-African populations [30], we also included the 25 non-African samples genotyped for all SNPs except this one in the diversity survey, leading to a total of 99 population samples (11,286 individuals) belonging to four continental regions (Africa, Europe, Asia and America) available for analysis.
Similar(27)
Genotypes for all SNP except those included in the BovineSNP50 Bead chip were masked and subsequently imputed for animals of the validation population.
Complete genotype information was retained for animals in the reference population, whereas genotypes were set to missing for animals in the validation population for all SNP except those included in the BovineSNP50 Bead chip (version 2).
For all these SNPs except SNP #3-6 ofe of the two individuals was homozygous by 454 sequencing, but heterozygous by Sanger sequencing (Additional file 5 Table S2).
Like all dog breeds the GSD has undergone selective breeding [28] and this may reflect why all the associated SNPs, except one (TLR5 G22A) were not in Hardy-Weinberg equilibrium.
Test for Hardy-Weinberg equilibrium suggested that the genotypes for all the SNPs except rs351224 (STRA6) were in Hardy-Weinberg proportions and there was no deviation from Hardy-Weinberg equilibrium.
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