Fig. 4

The impact of sequence context and event size on different graph-based genotyping methods. a Impact of breakpoint errors on genotyping (0 bp, 1 bp, 3 bp, 5 bp, 10 bp, 20 bp). b Impact of variant length (alternative allele length minus reference allele length) on genotyping. c Impact of number of SNPs and indels around breakpoints on genotyping. d, e Effects of repeat sequence types around breakpoints on genotype, partitioned by variant type: d deletions and e insertions. Different types of repeat sequences are annotated by RepeatMasker. 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. Detailed results are also provided in Additional file 2: Tables S9–S12