Fig. 2

The effect of heterozygous rate on the performance of different graph-based genotyping methods. The six ROC curve plots correspond to the genotyping results for synthetic heterozygous A. thaliana genomes with different heterozygous rates (0%, 0.27%, 0.52%, 1.03%, 2.07%, and 2.35%). The genome graph for genotyping is constructed from the A. thaliana reference genome and seven 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: Table S6