Characterization of SNP data sets.

A benchmark data set for evaluating methods for inversion detection using using SNP data was formed from data for three insect species (D. melanogaster [37, 38], An. gambiae and coluzzii [17, 39]). The chromosome arms were organized into three test cases (negatives, positive drawn from a single population, and positive drawn from multiple populations) based on known inversion genotypes from previous papers. We analyzed SNPs from the 2R chromosome arms of An. gambiae and coluzzii but do not include these data in our benchmark data set since not all inversions were fully characterized. For each chromosome arm, the geographic locations in which the samples were collected, species of the samples, number of samples, inversions identified in these data by the original authors and their frequencies, and the number of SNPs are provideded.