Figure 5.

The Deviation versus the Number of True Haplotypes; the Number of Unique Copy Units in the True Haplotypes; the Number of All Possible Haplotypes Consistent with the Count Data Sets; and the Unevenness of the True Haplotype Frequencies

The numbers of all possible haplotypes and the unevenness were arranged by the bin and plotted at the median point on the x axis. On the y axis, we plotted the median of the deviations (red for all haplotypes, blue for false-positive haplotypes) in each category that was composed of (at least 10) simulated data sets classified by the criteria indicated in the labels on the x axis and in the key.

(A) Results of the inference of only copy numbers.

(B–D) Results of the inference of copy unit combinations with variant bases.

(B) For the one SNVC site and the plain EM.

(C) For the three sites and the plain EM.

(D) For the eight sites and the PL-EM.