For each sample, for each base and for each potential type of mutation (i.e. substitution, one or two base deletion or one base insertion), the specificity was calculated as the ratio of the PM probe hybridization signal of the wild-type target to their cognate insertion, deletion or single base substitution probes on each strand. The logarithm of these ratios was plotted as a function of the position within the gene. To illustrate the special patterns and to smooth out random variation, running averages of data from 10 bases were used. To capture the variability, at each base, the sample-to-sample standard deviation was again calculated using data derived from a running average of 10 bases for each sample.