Table 1 Characteristics of the closest significant SNP for each method and each phenotype. For each method, the SNP location, its p-value and rank are provided for the tagSNP that is closest to the causal mutation. The columns labelled “Genotype distribution of cases” and “Genotype distribution of controls” detail the number of times a specific genotype (AA, AB or BB for di-allelic markers with alleles A and B) occurred for cases and controls, respectively. Whereas EG-GWAS was each time closer to the causal mutation, its result was less significant for furnishing because that tagSNP was only called in 8 out of 16 cases. This higher variability in call rate was expected based on earlier reports5,10 (see methods). Nevertheless, for EG-GWAS, the genotypes of cases and controls are perfectly separated whereas for cHD, there is an overlap of 1 sample for furnishing and 5 samples for hair length. Manhattan plots are presented in Suppl. Fig. S4.

From: An exome sequencing based approach for genome-wide association studies in the dog

Phenotype Technique SNP P-value Genotype distribution of cases (AA/AB/BB) Genotype distribution of controls (AA/AB/BB) Distance Rank
Hair length EG-GWAS chr32:4509367 1.87e-06 6/0/0 0/1/17 0 1
  cHD chr32:4299533 0.002 4/2/0 0/3/19 200 32
Furnishing EG-GWAS chr13:8611728 1.858e-05 8/0/0 0/0/12 1 3
  cHD chr13:8635445 4.601e-07 1/0/15 12/0/0 25 1