Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap and a white line is drawn through the black box representing the gap.
This assembly contains only one type of gap: contig gaps. These are gaps of 5000 bp between the scaffolds ("super-contigs") constructed from the whole genome shotgun (WGS) contigs. On the virtual chromosomes containing scaffolds that could not be confidently placed on a chromosome (e.g. chrUn and chrNA), 500 bp gaps have been inserted between scaffolds.