Three cases in computation of the 5′ clipping position of a read f. A vertical line shows the start position of an overlap between two reads. The thick line indicates the 5′ clipping range of f. The dot marks the start position of a high-quality region of f. The arrow points to the 5′ clipping position of f. Assume that cdep, the maximum number of overlaps that can be used for computing any clipping position, is set to 3. (A) The maximum depth of coverage by overlaps in the 5′ range of f, denoted by mdep5(f), is 0. (B) We have mdep5(f) = 2 < 3 = cdep. (C) We have mdep5(f) = 4 > 3 = cdep.