African Drosophila simulans population genomics

We have sequenced 22 isofemale (i.e., descendants from a single wild-caught female) lines of African Drosophila simulans. Strains were collected from Kenya (N=11) and from Madagascar (N=11), the putative ancestral location of the species. Flies from sixteen of these isofemale lines were inbred in the lab for approximately 10 generations of sibling mating. A 500bp short-insert library was constructed and sequenced by BGI using Illumina Hiseq 2000 (Illumina encoding 1.5) and paired-end sequencing, at an average coverage of 55X and read length of 90bp. Adapters in reads were deleted and reads which contained more than 50% low quality bases (quality value <= 5) were removed. The goal is to perform population genomic analyses of these lines.