AbstractRead alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality: the probability the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. We describe a framework for predicting mapping qualities that works by simulating a set of tandem reads, similar to the input reads in important ways, but for which the true point of origin is known. We implement this in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.