Next, we sought to uncover underlying trends in the hybridization specificity of different classes of mismatch probes across the entire ATM coding region within a given sample (intra-sample variation). This provides insights into sequence context effects that may influence the hybridization specificity of each class of mismatch probe. To approach this problem, we plotted the average hybridization specificity ratios of substitution, deletion and insertion probes for all 1168 bases across the 68 samples (Figure 4 and Supplementary Figure 1) . We analyzed data determined over running averages of 10 bases in order to maximize our ability to detect trends and minimize the effect of randomly dispersed confounding factors (e.g. intra-or intermolecular secondary structure) that may skew data for any given base.