Description

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. These are represented by varying numbers of Ns in the assembly. In this context, a contig is a set of overlapping sequence reads and a supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads. 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 1,000 and 3,000,000 Ns in the assembly. The beginning of chromosomes chr10, chr15, chr18, chr19, chr20 and chr21 are marked with non-bridged clone gaps of 3,000,000 Ns.

See also: Broad Institute assembly statistics.