Additional file 14.

Figure S9 - genotyping performance for simulated data. Estimates of true positive rate, false positive rate, and false discovery rate are provided for our four synthetic templates for all mapping strategies and mismatch conditions, based on 50× simulated read sets and genotyped using a Q ≥ 40 stringency cutoff. Estimates for the BESTNO-Q strategy (best no-guess mapping using read quality values for mapping) were based on default Bowtie settings (-n mode with -l 28 -e 70).

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Simola and Kim Genome Biology 2011 12:R55   doi:10.1186/gb-2011-12-6-r55