Targeted next-generation sequencing (NGS) focuses the sequencing effort by capturing and enriching regions of interest with complementary biotinylated probes. Though many factors can influence capture efficiency, a primary consideration is how well the DNA sequence of the probe matches the target, as this affects both the efficiency and selectivity of capture. This is especially important as probes are typically designed around a reference genome. To understand the factors that might influence high quality probe design, we examined the effects of the number and distribution of mismatches on capture efficiency in target enrichment, and provide strategies for modulating potential inefficiencies arising from probe design.