Fig. 1. Study design and summary of miracidia stage samples sequenced.

a Sampling was performed in two districts in Uganda; Mayuge district and Tororo district. Within those regions four schools were selected, three from Mayuge district which borders Lake Victoria: Bwondha (green), Bugoto (light blue) and Musubi (yellow). One school from the Tororo district, close to the Kenya border, was chosen: Kocoge (pink). Mayuge district and Tororo district primary schools in each region have been under long-term and short-term mass drug administration (MDA) pressure, respectively. b Pre- and post-treatment sampling information. Circles indicate the numbers of miracidia sampled at week 0 (immediately before treatment) and 4 weeks post-treatment, lines indicate miracidia sampled at both time points from the same children, only samples passing read sequence quality control are included.