Figure 2. Density plot of axis 1 eigenvalues from the Principal Components Analysis. Plots are based on candidate SNP genotypes from each of the 28 pooled whole genome resequencing libraries representing virus affected (red) and unaffected (black) fishing stocks.
Figure 3. (a) Regression analysis indicating a positive linear relationship between number of candidate SNPs (BF > 50) and scaffold length. Outlier scaffolds with a greater frequency of candidate SNPs relative to scaffold length are plotted in red. (b)Heatmaps of outlier scaffolds generated with the package LDBlockShow (Dong, et al., 2021) depicting the pairwise linkage disequilibrium measure of D ’ (refer to colour key) between each SNP with a BF ≥ 50. In addition, black triangle sections represent detected haplotype blocks; genomic regions of low recombination.