Description

This track depicts the gaps in the assembly (Oct. 2010, CGSC 2.1.3 (GCA_000001515.3)) of the chimp genome provided by the Chimpanzee Genome Sequencing Consortium.
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 the following principal types of gaps:

• Fragment - gaps between the contigs of a draft clone. (In this context, a contig is a set of overlapping sequence reads.) These may or may not be bridged.
• Contig - non-bridged gaps between map contigs.
• Centromere - non-bridged gaps from centromeres.
• Telomere - non-bridged gaps from telomeres.
• heterochromatin - non-bridged gaps from large blocks of heterochromatin.
• Short Arm - non-bridged long gaps on the short arm of the chromosome.
• Clone - gaps between WGS contig sequences, all indicated as bridged gaps, and found only on chromosomes chr7, chr21 and chrY
• Other - unknown sequence marked as 'N' nucleotides, not mentioned as a gap in the AGP files, all indicated as bridged gaps