This track shows regions of the human genome that are alignable to other Homo sapiens genomes. The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown with thin lines like introns. More description on this display can be found below.
Other assemblies included in this track are from the HPRC project.:
The chain track shows alignments of the human genome to other Homo sapiens genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both source and target assemblies simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.
The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the query assembly or an insertion in the target assembly. assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the target genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.
In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.
By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.
To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.