This figure illustrates the differences between univariate and multivariate segmentation. The upper panel shows univariate segmentation results, and the lower panel shows multivariate segmentation results. Red segments are probable deletions, while the blue segments are probable copy gains. (A-B) Rare copy gains and deletions detected only by univariate segmentation. (C) Small, common CNVs detected poorly by the univariate method, but with better resolution by the multivariate method. (D) This common CNV was ignored as an outlier by univariate segmentation, which considers only one subject at a time, because it is covered by only one marker. Multivariate segmentation, which simultaneously considers all subjects, was able to recognize that this single marker clearly has multiple copy states. (E) Large, common deletion that was accurately detected by both segmentation methods. The multivariate method provides better resolution of the segment endpoints.