Types of identified misassemblies. In A and B, black arrows correspond to the actual genome, and other lines to the assembly. (a) Major misassembly, wherein a single contig (or supercontig) contains sequence from disparate regions of the genome. (b) Three types of misassembly that can be corrected by reordering of contigs. Distinct supercontigs are colored yellow or turquoise. (c) Allelic regions are placed in tandem (top), instead of correctly into their respective haplomes (bottom). Haplome A sequence is shown in green and haplome B in blue. A sequence misjoin at the location indicated by the red arrow places the X region of haplome B into a haplome A contig. The haplome B supercontig contains an assembly gap in the X region.