Detecting inversions with PCA in the presence of population structure
Table 5
We evaluated a single methods (PCA with clustering) on the genotype inference task (which inversion genotype does a sample have?) using two benchmark test cases (positive from a single population and positive from multiple populations). Note that the two association-testing methods are not able to infer genotypes. For each chromosome arm used, we indicated known inversions, how many genotypes are present in the data set, and a measure of balanced accuracy calculated from the cluster predictions. The D. melanogaster 3R chromosome arm has three mutually-exclusive inversions, which we list separately.