Scaffold gap and error subgraphs. Diagrams follow the format of Figure 3. The rounded boxes represent extensions to the surrounding threads. Line ends not incident with the edge of boxes represent the continuation of a thread unseen. In each diagram the right end of block a and the left end of block b (if present) represent the ends of contig paths, and the enclosed gray thread represents the joining thread. The black thread represents a haplotype thread. The gray thread represents either a haplotype or bacterial contamination thread. (A) (Hanging) scaffold gaps and hanging insert errors. (B) Scaffold gaps and indel errors. (C) Intra- and interchromosomal joining errors and haplotype to contamination joining errors.
