Genome assemblies reveal the structure and frequency of variants underlying visible phenotypes. (A) Contiguity plot comparing the ISO-1 release 6 contig-level reference assembly with the 11 de novo genome assemblies generated in this study. (B) Minor allele counts for large SVs (LSVs; >100 bp), small SVs (SSVs; 11–100 bp), nonsynonymous SNPs (nsSNPs), and synonymous SNPs (sSNPs). (C) Gene and TE content of the duplicated sequences at the Bar locus (ISO-1 coordinates X: 17,334,493–17,537,993), which contains nine complete genes and one truncated gene (CG4368). A roo element (circle) separates the two copies, consistent with the hypothesized mechanism of TE-mediated duplication. (D) The Dp(2;4)ey^D mutation is a translocation–duplication of a large segment of Chromosome 2L inserted into an exon of the eyeless gene on Chromosome 4, replacing 320 bp of coding sequence.