Fig 3. SmartMap and uniread analyses of the validation dataset.

Iteration 0 and iteration 1 refer to SmartMap analysis with 0 and 1 iterations of reweighting, respectively. Scored and unscored refer to whether alignment score was considered in analysis, per Methods. Dashed lines are presented for readability of overlapping curves rather than discontinuities in data throughout this figure. (A) Quantile plot of read depth at the true origin loci, with Gold Standard dataset and analysis conducted in (left) scored mode or (right) unscored mode. (B) Quantile plot of excess read depth in SmartMap datasets relative to corresponding uniread dataset at true origin loci in (left) scored mode and (right) unscored mode. (C) QQ plot of read depth at true origin loci in the SmartMap (1 iteration) scored dataset vs. uniread scored dataset. Color scale represents percentile of each point, from 1^st to 99^th percentiles. (D-E) Median (D) read depth or (E) excess read depth vs. mappability score (UMAP50) [25] of the true origin loci. (F-G) Average read depth (F) at true origin loci and (G) outside true origin loci. (H) Mean absolute error of read depth at true origin loci for each dataset, with Gold Standard as the reference point. (I) Mean proportion of alignments intersecting with the true read of origin for each weight after SmartMap with no reweighting (green) and one iteration of reweighting (red) in scored mode. Dashed line represents line with slope of unity. (J) Mean weighted overlap proportion score between alignments intersecting the true read of origin and the true read locus for each weight after SmartMap with no reweighting (green) and one iteration of reweighting (red) in scored mode. Weighted overlap proportion score is meant to represent the proportion of a read’s weight that maps to the correct location due to a particular alignment and is computed as a weighted geometric mean of the proportion of the alignment covered by the true read and the proportion of the true read covered by the alignment.