## Description

This track depicts gaps in the assembly.

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 supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap.

This assembly contains the following principal types of gaps:

- contig - gaps between the Whole Genome Shotgun contigs of a scaffold. (In this context, a contig is a set of overlapping sequence reads. A scaffold is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying numbers of Ns in the assembly. Fragment gap sizes are usually taken from read pair data.
- scaffold - gaps between scaffolds linked by the fingerprint map. In general, these are represented by 500 Ns in the assembly.
- centromere - gaps for centromeres were included when they could be reasonably localized. These are represented by 500,000 Ns in the assembly.
- other - unknown bases marked 'N' in the sequence that were not in the assembly AGP file definition of gaps.