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 annotated 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_random and chrNA_random), 50,000 bp gaps have been inserted between scaffolds. Note that, in addition to unannotated stretches of Ns represeting poor quality sequence or regions that were filtered out, there are also stretches of Ns at the ends of some scaffolds. These are arbitrary sequences of extra Ns that were appended after trimming WGS sequences attached to the ends of scaffolds.