6. Screening of the structural variant nearCYP6P5/CYP6P9b from whole-genome sequences from different regions of Africa
Based on the previous observations of the likely presence of an SV in the intergenic region between CYP6P9b and CYP6P5 (Mugenzi et al., 2019) due to the lack of amplification of the 1kb fragment, SV was searched using PoolSeq data from An. funestus populations available under European Nucleotide bioprojects PRJEB24384, PRJEB13485, PRJEB35040, PRJEB35040, PRJEB24351 and PRJEB10294 (Weedall et al., 2019, 2020) for 12 populations of An. funestus sampled across Africa from 2002 to 2016. These were aligned to the An. funestus F3 genome (Ghurye et al., 2019) using BWA (v0.7.17-r1188) (Li et al., 2009). Reads were coordinate sorted, and duplicates were marked with Picard (v2.18.15) (”Picard Toolkit,” 2019). The subsequent alignments were visually inspected for evidence of an insertion in the intergenic region of CYP6P5 and CYP6P9b in IGV. In addition, non-reference transposon insertions were searched for computationally using TranSurVeyor (v1.0) (Rajaby & Sung, 2018).