Quality score distribution in simulations. Quality scores are based on the Poisson method (Figures S6 and S7 in Additional file 1 for the Fisher exact and Empirical methods). Red dots represent the real LLMs, black dots represent the sequencing errors, and the size and color gradient of each dot is proportional to the frequency of the minor allele. Length of the read bins is 10 bp (see Figure S5 in Additional file 1 for results based on 5-bp read bins). (a) Coverage = 200×; (b) coverage = 500×; (c) coverage = 1,000×; (d) coverage = 2,000×.