Description
This track depicts gaps in the platypus sequence assembly.
Many of these gaps — with the
exception of intractable heterochromatic gaps — may be closed during the
finishing process.
Future improvements to the assembly will be
dependent on the availability of funding and improvements to existing
assembler software.
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 principal types of gaps:
- Fragment - gaps between the 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
assembly 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.
- Clone - gaps between supercontigs linked by the fingerprint map.
In general, these are represented by 100 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.
- Centromere - gaps for centromeres were included when they could be
reasonably localized. These are represented by 10,000 Ns in the
assembly.
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