The design and experimental performance of probe sets used to detect genome deletions. (A) A graphical representation of the data shown in Table 1. The number of probes in each of the nineteen staggered probe sets ‘designed’ to cover the phyB deletion of 104 bp in E124 line are shown with a sold black line. The numbers of ‘designed’ probes, that were experimentally ‘detected’ with normalized log2 intensities of less than −0.4 are also shown with a dashed black line. For example, in Figure 4B 8 of the 9 (88.9%) designed probes (staggered every 17 bp) covering the phyB deletion had a normalized signal log2 ratio of less than −0.4 in Figure 4B. These 17 bp staggered probe numbers designed and detected are shown in (A) by a black arrow. (B) and (C), are similar to (A), the number of probes in each of the nineteen staggered probe sets designed to cover the hy1 deletion of 28 bp in line E99 and the max2 deletion of 4 bp in line E99 are shown with a sold black lines and those experimentally detected with normalized log2 intensities of less than −0.4 are also shown with a dashed black lines, respectively. The staggered probe data for the max2 deletion (in line E207) >30 bp are not shown but the data is shown in Additional file 1: Figure S8.