Fig. 4

The performance measurements of variant-calling tools in different functional genomic regions of simulated data. a Boxplots showing the TPRs with minimal read depths ≥ 3 at inserted SNV loci in high-confidence regions. b Boxplots showing the false-positive rates according to the minimal read depths at inserted SNV loci in introns. c The scatter plot showing the log-transformed FDRs with minimal read depths ≥ 3 at inserted SNV loci in high-confidence regions. The black lines represent the log-transformed median values of FDRs. The criteria of RefSeq, which we used to annotate coding regions, are more stringent than UCSC, which we annotate exons. Therefore, the performances are slightly different in exons and coding regions. d Boxplots showing the F-scores with minimal read depths ≥ 3 at inserted SNV loci in high-confidence regions