Detection of copy number variation and single nucleotide polymorphisms in genes involved in drug resistance and other phenotypic traits in P. falciparum clinical isolates collected from Uganda

► P. falciparum CNP and SNP containing genes may influence key parasite phenotypes. ► Pfmdr-1, gch1 or novel gene amplifications were absent in P. falciparum isolates. ► Mutations in Pfmdr-1 and Pfcrt genes were not associated with clinical outcome. ► Continued surveillance for changes in copy number and SNPs is essential. ► P. falciparum phenotypic variation may have a role in parasite virulence mechanisms.