This track shows pangenome local ancestry inference (pcLAI) for this Human Pangenome Reference Consortium (HPRC) Release 2 assembly, in the assembly's own coordinates. Every person's genome is a mosaic inherited from ancestors of different populations, and "local ancestry" is the assignment, region by region along a chromosome, of the most likely ancestral source of that stretch of DNA. This track divides each haplotype into windows and reports the ancestry inferred for each window, letting users see how ancestry varies along a single individual's genome.
Each item is one genomic window. The item name records the window and its inferred ancestry values, and the item color reflects the inferred ancestry, so that runs of shared ancestry appear as blocks of consistent color. The per-window inferred ancestry values are also shown on the details page. (The precise meaning of the numeric ancestry values and of the color mapping is defined by the pcLAI method; see Credits.)
Pangenome local ancestry inference assigns ancestry to windows along each assembled haplotype using a reference panel of population-labelled genomes. This track uses the assembly-coordinate (asm_coord) output, i.e. ancestry placed on each HPRC assembly's own sequence. Companion outputs projected onto GRCh38 and CHM13 coordinates are distributed separately.
The annotation files were obtained from the HPRC Release 2 data collection on the public s3://human-pangenomics bucket, indexed at the hprc_intermediate_assembly data tables. The per-assembly BED file was converted to a UCSC bigBed file. The build scripts are in the kent source tree.
For automated analysis, the annotation is stored in a bigBed-format file (pclai.bb) that can be read with the UCSC tool bigBedToBed. The original files are available from the HPRC S3 bucket linked above.
Annotations were generated by the Human Pangenome Reference Consortium. Thanks to the HPRC production team for making these data available.
A formal method citation for pcLAI is pending; details are maintained with the HPRC intermediate assembly resources. Data were generated by the Human Pangenome Reference Consortium.