Description

This track depicts gaps in the assembly of chrUn, the "unordered chromosome" for this browser. Gaps are represented as black boxes. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap. In this case, a white line is drawn through the black box representing the gap and the gap is labeled "yes".

This assembly contains the following types of gaps:

• Fragment - gaps within a scaffold.
• Contig - gaps between scaffolds. These gaps, represented by 1000 Ns, are placeholders between scaffolds that were added as part of the construction of chrUn. Because the order and orientation between the scaffolds is unknown, contig gaps are considered to be unbridged.

For a discussion of gaps and the JAZZ assembler see Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (Supplemental Materials). Science. 2002 Aug 23;297(5585):1301-10.