Fig. 2

Normalized mapping balance to normalized assignment balance (NMB-NAB) plot of a SNV sites with naive assignment method, b SNV sites with context-aware assignment method, c insertion and deletion sites with naive assignment method, and d insertion and deletion sites with context-aware assignment method. Each dot represent a variant site in HG002 chromosome 20. The simulated reads are aligned using Bowtie 2 and default parameters. The balance and bias subcategories are classified based on the position of the dots (“Biased-site classification” section). For visual clarity, sites with no correctly-mapped REF reads are omitted; the full plot including these sites is available as Additional file 1: Fig. S1