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

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Data schema/format description and download
Data last updated at UCSC: 2010-02-03


This track depicts gaps in the assembly.

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 types of gaps:

  • Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads. A supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying numbers of Ns in the assembly. Fragment gap sizes are usually taken from read pair data.

There are 119,126 fragment gaps in this draft assembly with a combined total of 54,196,184 bases of Ns. All these gaps are bridged gaps.