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

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Data last updated at UCSC: 2006-08-15


This track depicts gaps in the assembly. 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 scaffold. 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 scaffold 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 scaffolds linked by the physical map. In general, these are represented by 1,000 Ns in the assembly.