Below is a sample output file from the SNPscan plotting tool. The x-axis corresponds to chromosomes 1-22 and X. Each SNP dataset is arranged vertically within a large rectangle. The y-axis displays several kinds of information. Copy number values are represented in dots, color coded according to each SNP's genotype: AA or BB (homozygous calls, displayed in blue), AB (heterozygous calls, displayed in red), and NoCall (displayed in green). Loss of heterozygosity (LOH) is shown as gray bars, while p values for copy number changes are shown as yellow lines.

You can see that the bottom track is from a male (with a lower copy number on the X chromosome) with uniparental isodisomy on the long arm of chromosome 1 (note the blue region showing homozygosity, without any change in chromosome copy number). Visit the sample data page for instructions on how to generate this image.