Fig. 5

HiC-Pro quality controls. Quality controls reported by HiC-Pro (IMR90, Dixon et al. data). a Quality control on read alignment and pairing. Low quality alignment, singleton and multiple hits are usually removed at this step. b Read pair filtering. Read pairs are assigned to a restriction fragment. Invalid pairs, such as dangling-end and self-circle, are good indicators of the library quality and are tracked but discarded for subsequent further analysis. The fractions of duplicated reads, as well as short range versus long range interactions, are also reported