Analysis of the 188× coverage breast tumor PD4120a. (A) (Left) Read depth ratios (gray) and the copy number aberrations inferred by our algorithm when n = 3 including the normal population (black), dominant (clonal) tumor population (blue) and subclonal tumor population (red). (Right) A reconstruction of the tumor mixture with the inferred aberrations and estimated fraction of cells in each subpopulation. (B) Read depth ratios in 50 kb intervals after centering so chromosome 3 has a mean of 1 and correcting for 28% normal admixture using a simple linear scaling. (C) Virtual SNP array results showing distinct clusters of regions according to the number of reads containing each SNP and fraction of reads supporting the variant allele. (D) Virtual SNP array data comparing variant allele fractions and read counts for chromosomes 4 and 16. This data demonstrate that both chromosomes have undergone the same type of copy number aberration, which we predicted to be a clonal deletion in 72% of cells in the sample. (E) Virtual SNP array data for chromosomes 13 and 22. Chromosome 22q11.2-12.1 and chromosome 13 appear to be affected by the same type of aberration, which we predicted to be a subclonal deletion in 61.9% of cells in the sample. In contrast, 22q12.2-13.3 is different, and the data are consistent with a clonal deletion. See Additional file 1, Figure S13 for further details.