Description

This track depicts gaps in the assembly (Dec. 2011, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) of the mouse genome. These gaps - with the exception of intractable centromere 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.

This assembly contains the following principal types of gaps:

(In this context, a contig is a set of overlapping sequence reads.)
• Clone - gaps between clones (114 gaps).
• Contig - gaps between map contigs, various sizes (104 gaps).
• Telomere - 42 gaps for telomeres (100,000 Ns)
• Centromere - 20 gaps for centromeres (size: 2,890,000 Ns)
• Short_arm - 21 gaps for the short arm (10,000 Ns) at base positions 100,001-110,000 of each chromosome.
• other - sequence of Ns in the assembly that were not marked as gaps in the AGP assembly definition file, various sizes (384 gaps).
• Fragment - a single gap of 31 bases in chrX_GL456233_random.