We analyzed a total of 7772 short-read genomes after quality control. The plots show the breakdown across SV class and size. a) Overall, on average each genome carried 5,626 SV, with a median of 1361 insertions, 2991 deletions, 1194 duplications, 115 complex SVs and 11 inversions. b) The majority of SVs were small with a medium size of 329 bp. Overall only a total of 8% of SV per genome were larger than 2.5kb and 1% of SVs per genome were >50kb.