(B) The default method for calculating link coverage. Link coverage is necessary to normalize the observed counts for the length of the unique portions being linked and the insert size. The theoretical minimum and maximum insert sizes linking the two unique portions, represented as brown and green lines, respectively, are calculated and given the empirically determined insert size distribution, and the area under the curve between the minimum and maximum insert sizes is estimated. The link coverage equals the number of mate pairs linking the two unique portions over the ratio of this area to the area of the whole insert size distribution.