Figure 1.

A sequence used to make probe sets, reference sequence and a sample sequence are shown with an asterisk above the bases that match in prototype (generates probe sets) and sample sequences. Also shown are the reassembled model base-call results for each probe set for different values of m. Region A has 20 contiguous bases matching between sample sequence and reference sequence resulting in only N calls when m is >20. The longer region B has probe sets that make base calls up to m = 23. For each region, an increase of one or two in m results in one or two base calls at each edge to ceasing to make base calls. This occurs because it is no longer a fragment with sufficient matches. Region C has two contiguous regions of 9 and 12 bases with an SNP in between. One probe of the SNP set has 22 bases that match in the sample but no other probe in the region has more than 12 bases matching, therefore, all values of m return an N call.