Next generation sequencing (NGS) of mutant reporter transgenes is increasingly being used for mutation spectrum analysis (MSA) to characterize the genomic effects of mutagens. The ability to simulate NGS-MSA experimental data will permit the tuning of various parameters in the downstream analysis pipeline. However, no simulator currently exists that is capable of producing the read depths (up to 100,000x) required for MSA experiments. In this study, we introduce MutSim, a short read mutation simulator that enables researchers to generate NGS data for simulated samples exposed to a mutagen. MutSim generates data following the Ion Proton™ instrument error model and also a mutational model of a given mutagen. MutSim is shown to be highly scalable both with respect to genome length and read depth coverage. MutSim simulated data is validated against real experimental data in several aspects including genotype content, quality scores, read depth coverage and read length.