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

Display mode:   
View table schema
Data last updated at UCSC: 2011-05-10


This track depicts gaps in the draft assembly (Nov. 2009, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)) of the cow genome. 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 - Gap between sequence contigs.
  • contig - Gap between clone contigs. These are represented by 5,000 Ns in the assembly.
  • other - Unknown bases marked 'N' in the sequence that were not in the assembly AGP file definition of gaps.
See also: AGP specification