Counts of kākāpō structural variants (SVs) by type for unfiltered variants, those retained after SV quality filters and after genotype quality filters specific to each of the structural variant discovery tools Delly, Manta, Smoove, CuteSV and Sniffles. Delly, Manta and Smoove are short-read based, and CuteSV and Sniffles are long-read based, variant discovery tools.