Comparison of capture efficiencies. The efficiency with which each fragment of the selected area is captured was derived from counting all of the reads for any particular fragment, that is, all its interactions, its self-ligation, and non-cleaved material and plotting these against the presence of two, one, or no oligonucleotides (probes) in the fragment (A). This shows that the presence of one or two oligonucleotides does not make a difference in the capture as would be expected under conditions where the oligonucleotides are in saturation. When no oligonucleotides are present for a particular fragment, the number of reads will be lower, because the reads due to self-ligation cannot be captured. When the reads are corrected for the self-ligation and non-cleaved fragments this difference largely disappears (B). P values were calculated using the Mann–Whitney U test.