Benchmarking results for the original Illumina HiSeq 2500 and PacBio SMRT reads that were utilized for the assembly of UFRJ50816 in [23]. The solid curves ( +/- 0nt) and triangles benchmark the SV callers for their ability to rediscover the exact locations of breakends. The dotted curves ( +/- 25nt) and discs show the callers performance if we grant a tolerance of +/- 25nt for the breakends positions. Here, if an SV caller reports multiple entries within the emerging 50nt window, we pick the entry with the highest score and discard all remaining entries. Manta does not report different confidences and hence appears as single points in the analysis. For all other callers, curves are inferred by gradually adding calls to the analyzed set, in reverse order of their confidence. Gridss and Manta are designed to work with short reads (Illumina reads) merely and are therefore excluded from the PacBio benchmarking. The reported VCF BND-tags of Manta and Gridss are translated into corresponding matrix entries for benchmarking
