This track shows segmental duplications in this Human Pangenome Reference Consortium (HPRC) Release 2 assembly. Segmental duplications are large blocks of genomic sequence (typically longer than 1 kb) that occur in two or more nearly identical copies. They are hotspots for recurrent structural rearrangements and harbor many genes that have expanded in the human lineage, so their exact positions differ from person to person and are of particular interest in a pangenome. Each entry marks one copy of such a block together with the paralogous copy it aligns to.
Each item is one segmental-duplication region. Items carry no visible label: the paralogous region the item aligns to, the percent identity of the alignment, the aligned length and the number of satellite bases are shown when the mouse is held over an item, and the full set of per-duplication measures is on the details page. The paralogous region is given in the form sequence:start-end. The strand is the orientation of the paralogous copy relative to this one, so items on the minus strand are inverted duplications. The score is the fraction identity scaled to 0–1000.
Items are colored by percent identity, following the same scheme as the segmental duplication track on the human reference assemblies:
| Orange — 99% or more identity between the two copies. | |
| Yellow — 98% to 99% identity. | |
| Gray — below 98% identity. Within this range the shade tracks identity, so the darkest gray items are the closest to 98%. |
SEDEF reports both members of each duplicated pair, so most duplications appear twice, once at each copy. The original field marks which of the two the source considered the original call; the track configuration page has a filter on it if only one member of each pair is wanted.
Segmental duplications were detected with SEDEF, which finds pairs of homologous genomic segments by seeding on shared k-mers and extending and refining the alignments, then reports each duplicated segment pair with a set of alignment statistics (see reference below). The calls were produced by the Eichler laboratory as part of the HPRC assembly annotation.
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 SEDEF output was converted to a UCSC bigBed file, keeping the region coordinates, the paralog partner, and the main alignment statistics. The sequence name of the paralogous region is translated from the HPRC PanSN naming to the name shown elsewhere in the browser. The steps are described in the -makeDoc, +makeDoc, the build scripts are in the kent source tree, and the track configuration is in trackDb/contrib/hprc2annot.
Every duplication call in the source files is kept, with one exception. For HG00735 haplotype 2 (GCA_018472765.3) the SEDEF calls were computed against an earlier version of the assembly's contigs, so about 40,000 contig-level calls name sequences that do not exist in the assembly served here and could not be placed; the roughly 21,600 chromosome-level calls are unaffected, although about half of them name one of the missing contigs as their paralogous region, so on that assembly alone the partner is shown in the HPRC naming rather than translated. This is a version mismatch in the source data rather than something introduced in the conversion. It is the only assembly of the 462 where either happens.
For automated analysis, the annotation is stored in a bigBed-format file (segdups.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 and the Eichler laboratory. Thanks to the HPRC production team for making these data available.
Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018 Sep 1;34(17):i706-i714. PMID: 30423092; PMC: PMC6129265