2.7. Statistical analysis

Allele frequencies of technical replicates prepared from sixteen farm populations analysed by deep amplicon sequencing were compared using a Kruskal Wallis test in SPSS v24 (IBM) and the resistant allele frequencies obtained from pyrosequencing and deep sequencing were compared by Lin's Concordance Correlation Coefficient, calculated in SPSS with the syntax provided by https://gjyp.nl/marta/Lin.sps. r_c (CCC) values > 0.8 are classified as a near perfect agreement (r_c = 1, would represent perfect agreement). Populations were divided into geographical regions for analysis (map boundaries detailed in Supplementary Fig. S1). Binomial logistic regression analysis was carried out to calculate the increase in risk of identifying F200Y resistant alleles between regions using pyrosequencing results (R version 3.2.5). Hardy-Weinberg analysis was performed to determine whether the P200 locus was under active selection at the point of the study. Observed and expected homo/hetero-zygote frequencies were compared using a chi-squared analysis, performed in Microsoft Excel.