In the upper panel, 3D plots of the P-values for a window with variable size that slides across (i) the chromosome of Salmonella typhi CT18 from 1 bp, i.e., the start to 2.5 Mbp (Fig. 3A), (ii) the chromosome of Salmonella typhi CT18 from 2.5 Mbp to 4.8 Mbp, i.e., end (Fig. 3B). The P-value at a specific location and for a specific size of the window is plotted using a gray scale that changes gradually from black to white with black corresponding to the extreme P-value = 0 and white corresponding to the other extreme P-value = 1. The white dots corresponding to higher P-values are almost invisible in the white background while dark dots corresponding to low P-values are prominently visible marking the GIs in the chromosome. Lower panel in each figure gives some representative 1D plots generated from the refinement phase for some of the 'putative GIs' (enclosed in gray blocks and labeled as 1,2,... in the 3D plots) detected in the first phase of Design-Island. The quantity (P0-P-value)+ for the region of a GI detected in the first phase is plotted. Here, for P-value > P0, (P0-P-value)+ = 0, and for P-value < P0, (P0-P-value)+ = (P0-P-value).