Clustering of differential SNPs across strains. The analysis was performed on all differential SNPs falling within coding regions. Clustering was based on Euclidean distance of allele frequency variations as compared to the susceptible strain and complete linkage algorithm. Pie charts describe biological functions affected within main clusters based on the number of differential SNPs affecting transcripts assigned to each function. Stars indicate biological functions significantly enriched compared to their representation among all detected transcripts (Fisher’s test adjusted P value: * ≤ 0.05, ** ≤ 0.01, *** ≤ 0.001). For each cluster, the total number of differential SNPs is indicated as plain text while those affecting transcripts of known function (used for pie charts) are shown within brackets.