Sampling of different nucleosome configurations changes with extent of MNase digestion. Computer simulation of an MNase digestion titration depicting different technical preparations of chromatin including under-digested samples (15% and 50% Monos), normal-digested samples (75% Monos), and complete-digested samples (100% Monos). Graphs illustrate the normalized count (# sequence reads) of mono-nucleosome fragments aligned to the original template sequence after a simulated digestion and size selection (115–195 bp). All simulations were conducted on an identical template population with each template containing 6 equally sized nucleosomes (147-bp) with 100% occupancy. Each nucleosome was spaced 15-bp apart except for a central 142-bp linker and a larger upstream linker (30-bp). Nucleosomal protection of DNA is modeled to range from 50x to 1000x greater than naked (linker) DNA and relates to a base-pair’s location within a nucleosome, based on the in vivo work of Widom and colleagues (see Additional file 2: Figure S5) .