Table 5. Genotype inference task.

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.

Test Case	Chrom.	Inversion	Present Genotypes	Clusters	Balanced Accuracy
Single	D. mel. 2L	In(2L)t	3	3	93.3%
Single	D. mel. 2R	In(2R)NS	3	3	94.4%
Single	D. mel. 3R	In(3R)Mo		3	60.7%
Single		In(3R)p		3	43.3%
Single		In(3R)K		3	55.0%
Multiple	150 An. gam. and col. 2L	2La	2	3	66.7%
Multiple	81 An. gam. 2L	2La	2	2	100.0%
Multiple	34 An. gam. and col. 2L	2La	3	4	100.0%

We evaluated clustering in terms of accuracy of inferring inversion genotypes. Inversion genotypes were retrieved from the original papers describing the data [17, 37–39]. Association of the known genotypes with the cluster labels was measured using balanced accuracy. *Could not resolve multiple, mutually-exclusive inversions