Figure 1: Differences between the different sample libraries.

Libraries A, E and G are PCR-free. (a) GC bias of the different libraries. The genome was segmented into 10-kb windows. For each window, the GC content was calculated and the coverage for the respective library was added. For better comparability, the coverage was normalized by dividing by the mean. The major band in normal corresponds to autosomes, while the lower band corresponds to sex chromosomes. The increased number of bands in the tumour is because of a higher number of ploidy states in the (largely) tetraploid tumour sample. (b) Cumulative coverage displayed for different libraries. Displayed are all libraries sequenced to at least 28 ×. To make the values comparable, we downsampled all samples to a coverage of 28 × (the lowest coverage of the initially sequenced libraries). The plot shows the percentage of the genome (y axis) covered with a given minimum coverage (x axis). (c) Percentage of certain regions of interest covered with less than 10 ×. Different colours are used to distinguish centres.