Description
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 two types of gaps:
- fragment - gaps between the Whole Genome Shotgun contigs of a
supercontig/scaffold. (In this context, a contig is a set of
overlapping sequence reads.
A supercontig/scaffold 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.
- scaffold - 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.)
These are represented by 1,000 Ns in the assembly of
the artifical chromosome chrUn (concatenation of unplaced supercontigs).
Credits
The Jan. 2007 Pristionchus pacificus (5.0) draft assembly was
produced by the
Washington University School of Medicine GSC with the following
data use policy.