Table 1. Comparison of methods.

The capabilities of three PCA-based methods (PCA scatter plots with optional clustering and association testing SNPs against either cluster labels or PC coordinates) are summarized. We compare the methods on detecting, genotyping, and localizing inversions in terms of capability, easy of use, and potential for ambiguous results.

	PCA Scatter Plots	Clustering	Cluster-SNP Association Tests	PC-SNPAssociation Tests
Detects Inversions	Yes	Yes	Yes	Yes
Infers Inversion Genotypes	No	Yes	No	No
Localizes Inversions	No	No	Yes	Yes
Ease of Use	Easy	Moderate	Difficult	Easy
Potential for Ambiguous Interpretation	Yes	Yes	No	No