The mosquito Anopheles gambiae ss. is distributed across most of sub-Saharan Africa and
is of major scientific and public health interest for being an African malaria vector. Here we
present population genomic analyses of 111 specimens sampled from west to east Africa,
including the first whole genome sequences from oceanic islands, the Comoros. Genetic
distances between populations of A. gambiae are discordant with geographic distances but
are consistent with a stepwise migration scenario in which the species increases its range …

Results Sequencing, pre-processing of sequence data, mapping, and variant calling.
Sequencing of the 111 samples resulted in 3.7 billion reads in total with a mean genome
coverage of 11.7× per sample (Supplementary Table 1). On average, 95.6% of the reads
were mapped onto the reference genome AgamP4 38 by BWAMEM 39. Applying joint
variant calling with Freebayes 40, we identified 24,069,835 high-quality biallelic single-
nucleotide polymorphisms (SNPs) in the dataset.