Description
This track depicts gaps in the zebrafish assembly. These gaps - with the
exception of intractable heterochromatic gaps - will 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 known, it is a bridged gap and a white line is drawn
through the black box representing the gap.
This assembly contains only one type of annotated gap: contig gaps. These
are gaps of 5000 bp between the scaffolds ("super-contigs")
constructed from the whole genome shotgun (WGS) contigs.
On the virtual chromosomes containing scaffolds that could not be
confidently placed on a chromosome (e.g. chrUn_random and chrNA_random),
50,000 bp gaps have been inserted between scaffolds.
Note that, in addition to unannotated stretches of Ns represeting poor quality
sequence or regions that were filtered out, there are also stretches of Ns
at the ends of some scaffolds. These are arbitrary sequences of
extra Ns that were appended after trimming WGS sequences attached to the
ends of scaffolds.
|