Haplotype alignments.

A) Alignment of phased variants from within the Ace1 duplication region (2R:3,436,800–3,639,600), using 345 samples from West African populations (Anopheles gambiae 1000 Genomes) with Ace1 duplications (Guinea A. gambiae, Côte d’Ivoire A. coluzzii, Ghana A. gambiae and A. coluzzii, Burkina Faso A. gambiae and A. coluzzii). B) Id., from a region downstream of the duplication (5 kbp starting at 3,639,600). C) Id., from a region upstream of the duplication (50 kbp starting at 3,436,800–1 Mb). D) Id., from a region downstream of the duplication (50 kbp starting at 3,639,600 + 1 Mb). (XLSX)