Description
This track depicts gaps in the assembly. These gaps - with the
exception of intractable heterochromatic gaps - will 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 known, it is a bridged gap and a white line is drawn
through the black box representing the gap.
There are four principal types of gaps:
- Fragment - gaps between the contigs of a draft clone.
(In this context, a contig is a set of overlapping sequence reads.)
These are represented
by 100 N's in the assembly, whether or not there is bridging information.
- Clone - gaps between clones in the same map contig. These are represented
by 50,000 N's in the assembly if the gap is bridged, or 100,000 N's if it is not.
- Contig - gaps between map contigs. These are represented by 200,000 N's in the assembly.
- Heterochromatin - gaps from centromeres (3,000,000 N's) or other large blocks of heterochromatin (size varies).