Fig. 3

Boxplots illustrating the Matthews correlation coefficient values by alignment, variant calling or padding method. a Entity of variants. b exonic SNVs. c exonic indels. d intronic SNVs. e intronic indels. Each dot represents one observation and horizontal bold lines denote median MCC values. Boxes extend from the 25th to the 75th percentile of each group’s distribution of values. Vertical extending lines (whiskers) denote the upper and lower adjacent values. Statistical analyses were performed using the non-parametric Kruskal–Wallis or one-way ANOVA tests. All box plots of MCC values, including not statistically significant correlations, are shown in Additional file 7. GATK Genome Analysis ToolKit, HC HaplotypeCaller, UG UnifiedGenotyper