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.

附加文件1：表S1。标题：基因型数据质量控制。描述：基因型数据来源于攻毒试验第16天仍存活的1972头实验动物。基因型数据通过580K Affymetrix® Axiom® HD基因分型阵列生成。检出率（call rate）阈值设置为98%，所有检出率低于98%的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）与样本均被排除。次要等位基因频率阈值设置为1%，低于该阈值的实验动物被剔除。基于R语言robustbase包中adjbox函数对偏态分布校正后的F统计量分布，评估杂合子过剩情况。本次分析同时排除了对照动物。在本次质量控制流程中，原580,961个SNP中共计138,568个被移除。