Table 1.

AUC for alignment score, alignment score per matched chunk, and M-Score

Error setting	Score	Score per Matched Chunk	M-score
Low	0.982	0.997	0.995
Medium	0.918	0.994	0.991
High	0.664	0.881	0.965

The AUC for discriminating true alignments from false alignments using the alignment score, alignment score per matched chunk, and M-score statistics for simulated Rmaps from the human reference under low, medium and high error settings. M-Score is comparable to the other methods under the low and medium error and performs superiorly under high error.