Visualising nucleotide diversity across the 4.3-kb SV
Alignments were re-created with the An. funestus F3 genome (VectorBase release 57, Ghurye et al., 2019) for Tororo (Uganda), Mibellon (Cameroon) and Obuasi (Ghana) populations using BWA (v0.7.17-r1188) (Li et al., 2009). Reads were coordinate sorted, and duplicates were marked with picard (v2.27.2) (“Picard Toolkit,” 2019). Pileup files for each population were created using Samtools (v1.6) (Li et al., 2009) with minimum phred-scaled base quality of 10 and mapping quality per read of 20. Population genetic statistics nucleotide diversity and Tajimas’ D were generated for 1000 bp non-overlapping windows across chromosome 2 using npstat (v1.0) (Ferretti et al., 2013) for each population separately. Plots of nucleotide diversity from positions 8,525,000 to 8,575,000 incorporating the rp1 resistance locus and 4.3 kb insertion site between CYP6P5 and CYP6P9bwere created using the karyoploteR package (v1.16.0) in R version 4.0.3 (Gel & Serra, 2017). A ratio of nucleotide diversity between Uganda and Cameroon, Ghana as two closely-related populations (Weedall et al., 2020) and susceptible FANG populations was plotted, and an upper-bound of 100 was arbitrarily chosen for 1kb windows of very low, or zero, diversity in order to plot the pattern of diversity across the region.