(C) The degrees of freedom method for determining link coverage. Here given a read length and insert size of 3 and two exons that are 6 and 5 bases long, there are three mate pair alignments that can link these two exons. Therefore, the degrees of freedom refer to the theoretical number of positions where a mate pair (given, in this case, 3+3+3 = 9 bp long fragment size) exists that links these exons on the mRNA, shown as black lines. The link coverage is the number of mate pairs linking the exons over the degrees of freedom.