Description
This track shows the gaps in the Feb. 2011 $organism genome assembly.
Genome assembly procedures are covered in the NCBI
assembly documentation.
NCBI also provides
specific information about this assembly.
The definition of the gaps in this assembly is from the
AGP file delivered with the sequence. The NCBI document
AGP Specification describes the format of the AGP file.
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:
- short_arm - short arm gaps (count: 4; size range: 11,330,000 - 16,000,000 bases)
- heterochromatin - heterochromatin gaps (count: 13; size range: 50,000 - 15,000,000 bases)
- centromere - gaps for centromeres are included when they can be reasonably localized (count: 24; size range: 100,000 - 3,000,000 bases)
- telomere - telomere gaps (count: 42; size range: 1,516 - 114,098,230 bases)
- contig - gaps between contigs in scaffolds (count: 2,853; size range: 1 - 1,650,870 bases)
- fragment - gaps between whole genome shotgun contigs (count: 18,623; size range: 10 - 3,000 bases)
- other - gaps added at UCSC to annotate strings of Ns that were not marked in the AGP file (count: 161,551; size range: 1 - 55,857 bases)