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

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Data schema/format description and download
Assembly: Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1)
Data last updated at UCSC: 2008-08-05

Description

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 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 one hundred Ns in the assembly.
  • Contig - gaps between supercontigs not linked by the fingerprint map, but instead by marker data. (In this context, the "Contig" gap type refers to a map contig, not a sequence contig.) In general, these are represented by 100 Ns in the assembly for all chromosomes except chrUn (concatenation of unplaced supercontigs), where gaps of 25 Ns are used.
  • Centromere - gaps for centromeres were included when they could be reasonably localized. Only one centromere is located in this assembly on chrZ and it's represented by 500,000 Ns.