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Gap Locations   (All Mapping and Sequencing tracks)

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Data schema/format description and download
Assembly: Mouse Jun. 2020 (GRCm39/mm39)
Data last updated at UCSC: 2020-07-27


This track shows the gaps in the Jun. 2020 mouse genome assembly.

Genome assembly procedures are covered in the NCBI assembly documentation.
NCBI also provides specific information about this assembly.

The definition of the gaps in this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file.

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:

  • centromere - gaps for centromeres are included when they can be reasonably localized (count: 20; all of size 2,890,000 bases)
  • short_arm - a gap inserted at the start of an acrocentric chromosome (count: 21; all of size 10,000 bases)
  • telomere - telomere gaps (count: 42; all of size 100,000 bases)
  • contig - gaps between contigs in scaffolds (count: 60; size range: 8,000 - 500,000 bases)
  • scaffold - gaps between scaffolds in chromosome assemblies (count: 181; size range: 27 - 522,000 bases)