Description

This track depicts gaps in the draft assembly (Nov. 2009, US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1)) of the $organism genome. 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.
Other - gaps that were not annotated in the AGP file for the assembly release. These are represented by Ns in the assembly.