Balancers are primarily chromosomal rearrangements that allow lethal or sterile mutations to be stably maintained as heterozygotes. Strains with balanced lethal/sterile mutations are available at the Caenorhabditis Genetics Center. Such strains harbor morphological markers, with associated molecular changes, that are intransto the balancer. In many cases, only the genetic position (in cM) has been described for balanced mutations or morphological markers. We used short-read whole genome sequencing to uncover the genomic position of those variants (balanced mutations and linked markers) and predicted their effect. We investigated 12 different strains, and characterized at a molecular level 12 variants.