Fig. 3

The effect of genome number on the performance of different graph-based genotyping methods. The five ROC curve plots correspond to genotyping results with different numbers (1, 7, 15, 30, 50) of graphed genomes. The genome graph for genotyping is constructed from the A. thaliana reference genome and different numbers of alternative genomes. Paired-end (2 × 150 bp) short reads with 30× depth are simulated for genotyping. For each genotyper, precision is plotted against recall as the genotyping quality threshold varies. Read depth on variant sites is used as a substitution score when genotype quality is not available. Arrows indicate the circles hidden by other circles in the plot due to identical or nearly identical precision values. Detailed results are also provided in Additional file 2: Tables S7–S8