Conformance checking techniques compare process models of organizational behavior with observed process executions to reveal their deviations. Traditional alignments concern individual activities and provide a single out of potentially infinitely many explanations for observed deviations. Skip alignments lift insights to subprocesses and provide all possible explanations. Though valuable for analysts and process mining tools, there exist no interpretations how likely these deviations are. In this paper, we introduce skip probabilities revealing how likely certain subprocesses deviate w.r.t. an event log of observed process executions. We show the formal derivation of this calculation and demonstrate the feasibility of its computation. By analyzing a realistic case, we empirically show that yet hidden process insights can be derived from skip probabilities and how they contribute to targeted process improvement.