## Description

This track depicts gaps in the assembly. Many of these gaps — with the exception of intractable heterochromatic gaps — may be closed during the finishing process.

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:

- Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads. A supercontig 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.
- Clone - gaps between supercontigs linked by the fingerprint map. In general, these are represented by 10,000 Ns in the assembly.
- Contig - gaps between supercontigs not linked by the fingerprint map, but instead by marker data. (In this context, the "Contig" gap type refers to a map contig, not a sequence contig.) In general, these are represented by 10,000 Ns in the assembly for all chromosomes except chrUn (concatenation of unplaced supercontigs), where gaps of 1,000 Ns are used. Gaps of other sizes were used when mRNA or other data suggested possible but not confirmed links between supercontigs.
- Centromere - gaps for centromeres were included when they could be reasonably localized. These are represented by 1,500,000 Ns in the assembly for the macrochromosomes 1-10 and Z, and by 500,000 Ns for all others (microchromosomes).