Description

This track depicts gaps in the $organism sequence assembly. Many of these gaps — with the exception of intractable heterochromatic gaps — may be closed during the finishing process. Future improvements to the assembly will be dependent on the availability of funding and improvements to existing assembler software.

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 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 assembly 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 100 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 100 Ns in the assembly.
Centromere - gaps for centromeres were included when they could be reasonably localized. These are represented by 10,000 Ns in the assembly.