Gap Track Settings
 
Gap Locations   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2012-04-13

Description

This track shows the gaps in the Aug. 2011 pig 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:

  • clone - gaps between clones in scaffolds (count: 5,323; all of size 50,000 bases)
  • other - gaps added at UCSC to annotate strings of Ns that were not marked in the AGP file (count: 14,502; size range: 1 - 109 bases)
  • fragment - gaps between whole genome shotgun contigs (count: 163,796; all of size 100 bases)