Structural variants are enriched in deleterious visible phenotypes in .

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 strains using highly contiguous genome assemblies generated with Oxford Nanopore long reads.