Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments (i.e. the region between one restriction site and the next).

This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or "dangling-ends". If not given, such statistics will not be available.

Sequence left by the restriction enzyme after cutting. Each restriction enzyme recognizes a different DNA sequence and, after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. For DpnII, the restriction site and dangling end sequence are the same: GATC. This information is easily found on the description of the restriction enzyme. The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol.

Number of lines to consider for the qc test run.