Normalization allows absolute copy number estimate after normalization, assuming the male pool is diploid across all autosomes. Left: female pool (blue). Right: UMC-11 (red). A and D: genome-wide distribution of the ratios of the number of reads aligning in each 150 kb window relative to the number in the same window from the male pool. B and E: counts are normalized by the total number of unambiguously aligned reads from each sample. C and F: counts are normalized by the mode from the distribution in B and E. Copy number of 1, 2, and 3 can be clearly seen in the UMC-11 sample.
Castle et al. BMC Genomics 2010 11:244 doi:10.1186/1471-2164-11-244