Estimated α for HME samples. Analysis of five hemimegalencephaly (HME) samples. (A) Estimated α values are shown as box plots. (B) BAF distributions of HME call sets. Each point represents one predicted somatic mutation in the corresponding sample. BAF was calculated from predicted heterozygous (orange) and homozygous (green) somatic mutations and loss of heterozygosity (LOH) sites. The mean BAF is consistent with the estimated α for every sample. The BAF calculated from read counts (red triangles) and mass spectrometry peak intensities (blue squares) of three previously validated mutations (MTOR, AKT3 and PI3KCA) are bounded in the predicted BAF ranges. BAF, B allele frequency; HME, hemimegalencephaly; LOH, loss of heterozygosity.