Description

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.

Display Conventions and Configuration

Chain Track

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.

Methods

The bigChain files were obtained from the HPRC S3 bucket (Amazon Web Services). For more information about how the bigChain files were generated, please refer to the HPRC publication below.

Credits

Thank you to Glenn Hickey for providing the HAL file from the HPRC project.

References

Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ et al. A draft human pangenome reference. Nature. 2023 May;617(7960):312-324. DOI: 10.1038/s41586-023-05896-x; PMID: 37165242; PMC: PMC10172123

Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol. 2023 May 10;. DOI: 10.1038/s41587-023-01793-w; PMID: 37165083; PMC: PMC10638906

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. DOI: 10.1038/s41586-020-2871-y; PMID: 33177663; PMC: PMC7673649

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep;21(9):1512-28. DOI: 10.1101/gr.123356.111; PMID: 21665927; PMC: PMC3166836