Structural variant (SV) counts per kākāpō chromosome as called using short-read, (Delly, Manta-Batch, Manta-Joint, Smoove), and long-read (CuteSV, Sniffles) based tools. For each, call sets were filtered for SV quality and the number of SVs per chromosome (A), and the proportion of chromosome base-pairs impacted by structural variants (B) were estimated. Chromosomes are ordered left to right by size (1-23), as per the naming convention for the kākāpo reference genome, excluding the Z and W sex chromosomes. The largest chromosome, chromosome 1, consistently carried the highest number of SVs detected in all six datasets. However, the smallest chromosomes consistently had the highest proportion of base pairs impacted by SVs (i.e., sum of all SV lengths / chromosome size) in all six datasets.