Fig 2. Characteristics of validation dataset.

(A) Schematic outlining the workflow to validate and optimize SmartMap. A set of six million randomly selected 200bp loci were used to simulate paired end reads. The true read depth distribution was then compared to both uniread and SmartMap analyses, with each analysis conducted in both “scored” and “unscored” modes, per Methods. (B, C) Number of (B) alignments or (C) reads vs. number of alignments per read for the validation datasets. (D) Mean absolute error of read depth at true origin loci in SmartMap scored mode vs. number of reweighting iterations (E) Genome browser view showing the read depth in the (top) uniread, (center) SmartMap (0 iterations), and (bottom) SmartMap (1 iteration) datasets of an example locus.