Fig 4. Alignment optimization.

Interaction maps for deletion sites identified from the deletion dataset of synthetic reads for BWA-MEM alignment with (A) default parameters and (B) optimized algorithm. The optimized analysis incorporates custom BWA-MEM parameters, ambiguous site removal, and exact edge matching. Points correspond to specific 5’ and 3’ deletion sites and are colored by the percent of total deletion sites correctly mapped to a specific nucleotide pair (see scale). (C) Summary of accuracies pre- and post-optimization for synthetic deletion (left) and deletion-insertion (right) datasets. See Methods for full summary of improvement.