This track shows point cloud 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" describes, region by region along a chromosome, where a stretch of DNA came from. Rather than picking one population label per region, PCLAI places each region on a continuous scale, so ancestry that sits between two reference populations is not forced into one of them. This track divides each haplotype into windows of 1000 SNPs, roughly a hundred thousand bases, and reports the ancestry inferred for each one, letting users see how ancestry varies along a single individual's genome.
Each item is one genomic window. Items carry no visible label. Holding the mouse over an item shows the window identifier, the position of the window in the principal-component space that PCLAI uses to describe ancestry, the ancestry the window is assigned to if that continuous position is discretized, and a confidence score; the same values are on the details page, together with a scatterplot showing where the window sits relative to the reference haplotypes that define the space. The item color is derived from the principal-component position, so windows of similar inferred ancestry get similar colors and a run of shared ancestry appears as a block of consistent color. Because the color is continuous rather than a set of population labels, it is read by comparing regions with each other rather than against a fixed legend.
Neighboring windows inside one block of shared ancestry differ by only one or two color steps. Those small differences are not meaningful: the feature to read is the block, not the window. Two consequences are worth knowing before concluding that a display looks wrong. First, a haplotype with a single ancestry throughout gives one uniform color across every chromosome, which is the correct result for that sample rather than a rendering problem. Second, where a haplotype does carry several ancestries the blocks are tens of megabases long, so a view of only a few megabases usually falls inside one block and also looks uniform. Zooming out to a whole chromosome is what makes the block structure visible.
Assembly GCA_018466835.2 (sample HG02257) is a useful example of a haplotype with several ancestry blocks. Its chr17 crosses four blocks, with transitions near 10.0 Mb, 50.7 Mb and 73.3 Mb, and chr5 crosses four more across its 184 Mb; chr20 and chr22 each cross three. In that same assembly chr2, chr13 and chr18 carry a single ancestry from end to end and are uniform in color, so picking one of those chromosomes gives no sense of what the track shows.
The track is best viewed in pack mode. In dense mode the windows are collapsed onto one row, which hides the per-window values.
Conventional local ancestry inference gives every segment of a genome one of a fixed set of population labels. Point cloud local ancestry inference instead places each segment at a point in a continuous coordinate space, so a genome becomes a cloud of points, one per window. The coordinate space can be any continuous description of ancestry; here it is the first two principal components of a reference PCA embedding built from 3122 1000 Genomes haplotypes of 21 populations of known origin. Ancestry that falls between the reference populations, which a label-based method has to round to the nearest label, therefore stays visible as an intermediate position. Each haplotype is split into windows of 1000 SNPs and a coordinate is predicted for each, with a confidence score; windows of very low confidence are dropped before the files are published. The files also carry a discretized version of each prediction, written as the PCA centroid of the ancestry cluster the window falls in, which across the whole release takes only four values. See the reference below for the method. This track uses the assembly-coordinate (asm_coord) output, that is, 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, with the window identifier and the predicted coordinate split out of the source item name into their own fields and the source's centroid column named. The steps are described in the makeDoc, the build scripts are in the kent source tree, and the track configuration is in trackDb/contrib/hprc2annot. Every window in the source files is carried through to the bigBed.
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.
Geleta M, Mas Montserrat D, Ioannidis NM, Ioannidis AG. Point cloud local ancestry inference (PCLAI): continuous coordinate-based ancestry along the genome. bioRxiv. 2026 Mar 25. doi: 10.64898/2026.03.23.713813