Description
This track depicts gaps in the draft assembly (Jan. 2011, Broad Institute of MIT and Harvard Orenil1.0 (GCA_000188235.1))
of the $organism genome.
*** Developer: remove this statement if no future assemblies are expected:
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 principal types of gaps:
*** Developer: make sure this part is accurate. Here is a WUSTL template:
- 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 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 10,000 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 10,000 Ns in the assembly for all
chromosomes except chrUn (concatenation of unplaced supercontigs), where
gaps of 1,000 Ns are used. Gaps of other sizes were used when mRNA or
other data suggested possible but not confirmed links between supercontigs.
- Centromere - gaps for centromeres were included when they could be
reasonably localized. These are represented by 1,500,000 Ns in the
assembly for the macrochromosomes 1-10 and Z, and by 500,000 Ns for
all others (microchromosomes).
*** Developer: here is a Broad template:
- Fragment - gaps between the Whole Genome Shotgun contigs of a
supercontig. These are represented by varying numbers of Ns in the
assembly. In this context, a contig is a set of overlapping sequence reads and
a supercontig is a set of contigs ordered and oriented during the
Whole Genome Shotgun process using paired-end reads. Fragment gap sizes
are usually taken from read pair data.
- Clone - gaps between supercontigs linked by the physical map.
In general, these are represented by 1,000 Ns in the assembly.
*** Developer: look for this kind of gap placement:
Clone gaps of 3,000,000 have been placed at the end of chrX and at the
beginning of all other chromosomes.