Fig. 3
From: Measuring, visualizing, and diagnosing reference bias with biastools
Bias-by-allele-length plots if we consider only Simulation Balance (blue), Mapping Balance (orange), Assignment Balance using context-aware assignment (green), and the same using naive assignment (red). Variant length varies along the x-axis, with positive values standing for insertion and negative values for deletions, and 0 for SNVs. The alignment is done by Bowtie 2 on HG002 simulated data. Top: Balance for all four measures. Dots represent median of the distribution and the whiskers indicate the first and third quartiles. Middle: Zoom-in on Mapping Balance and context-aware Assignment Bias with data normalized by subtracting median SB in each stratum. Bottom: number of variants with each length. Gaps exceeding 25 bp are collapsed into the \(-25\) or 25 strata