MOESM1 of Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers

Additional file 1: Table S1. Title: Quality control of genotype data. Description: The genotype data were obtained from 1972 animals that were alive at day 16 of the challenge study. Genotype data were produced using 580 K Affymetrix® Axiom® HD genotyping array. The call rate threshold was set at 98 %, and all SNPs and samples with values less than 98 % were excluded. The minor allele frequency threshold was set at 1 % and animals with values less than 1 % were excluded. Heterozygote excess was assessed based on the distribution of F-statistics adjusted for skewness using adjbox function from the R package robustbase. Control animals were also excluded from the analysis. A total of 138,568 SNPs out of 580,961 were removed during the quality control.