Types of misassemblies. (A) Three types of simple minor misassemblies are shown: insertions, deletions, and hanging ends. In all three cases, a contiguous segment (of a contig or the genome) of length less than 10 kb does not align in the expected location (with the genome or contig). This segment could be aligned at some alternate location in most cases, although we do not do this in practice. Compound minor misassemblies (e.g., contigs having two insertions) are reported as multiple misassembly events. (B) Two types of major misassemblies are shown. In the first type, two pieces of a contig align to distant parts of the genome (if one piece is very short, we instead report a hanging end, as in A). In the second type, adjacent contigs in a supercontig are aligned to distant parts of the genome. In practice, what we typically encounter is a hybrid between these two types: a contig that lies in the middle of a supercontig is split as in the first type. We call this hybrid the standard major misassembly.
