To make a copy number distribution plot similar to Figure 1B of Zhao et al. 2005, select "Chromosome/Summary Plot" at the inferred copy number view. The copy number thresholds outside which a sample is counted as gain or loss at a SNP are specified at "Tools/Options/Chromosome/Curve Min or Max". Specify a cytoband file at “Analysis/Chromosome” to show dotted lines marking the centromeres.

[Version 2/26/06+] The thresholds (Min and Max at “Options/Chromosome”) will be divided by 2 before comparing to chromosome X copy number in male to count gain or loss. For example, if Min is 1 and Max is 3, copy number =< 0.5 or >= 1.5 are counted.

[V12/22/06+] At the chromosome view, use “Chromosome/Show All” to toggle between displaying all chromosomes or just one chromosome, and then select “Chromosome/Summary Plot” to draw summary plot for all or one chromosome.

[V11/29/07+] If showing LOH in copy number view is on, UPD will be displayed in the copy summary plot, with black color representing UPD proportion: