Figure 5. A case study for the inconsistency of the alignment results with loose setting (5 edit costs at most) where BWA successfully finds an alignment for the read W while CGAP-align* fails.

The red color on the first line indicates the edit operations in the alignment found by BWA. In this particular alignment, we have 2 gaps and 2 mismatches. According to the cost metrics used during the alignment stage where the cost of gap extension is considered as 0, we need 4 edit costs to map W to X, satisfying the loose setting. The D-arrays calculated by BWA and DCDC are listed below. Both of them are strictly correct under D-array's cost metrics where the cost of a gap extension is 1.