+This track displays structural variants (SVs) — deletions, insertions, and +complex substitutions of at least 50 bp — from the Arabic Pangenome +Reference (APR), a pangenome graph built from 53 UAE-resident Arab +individuals drawn from eight countries (UAE, Saudi Arabia, Oman, Jordan, +Egypt, Morocco, Syria, Yemen). Each bubble in the graph that contains an +SV-sized alternative allele is shown as a single variant site, with allele +counts aggregated across the 53 samples (the GRCh38 reference haplotype, +present as an extra sample column in the source VCF, is excluded from the +aggregation).
+ ++The APR pangenome was built on the T2T-CHM13v2 reference. Variants are +shown natively on the hs1 browser and lifted to hg38 using +the UCSC hs1ToHg38.over.chain.gz chain; variants that do not lift +cleanly (often in T2T-added euchromatic sequence) are omitted from the +hg38 version of the track.
+ +Items are colored by SV type:
+Each item spans from the start of REF to its end on the reference. +The name field is the graph snarl ID (e.g. <951452<1012008), +which identifies the variant site in the APR pangenome graph.
+ ++The source VCF is multi-allelic: a single graph snarl appears as one row +with a comma-separated ALT list. For this track, each ALT is classified +individually using the 50 bp threshold, and the row is emitted as a single +bed item with:
+Rows whose alts are all smaller than 50 bp are not shown.
+ ++The APR pangenome was assembled from 53 individuals sequenced with an +average 35× PacBio HiFi, 54× ultralong ONT and 65× Hi-C +coverage, producing haplotype-phased de novo assemblies with N50 > 124 Mb. +The pangenome graph was built with Minigraph-Cactus v2.7.2 seeded on +CHM13v2 (backbone) and GRCh38; variants were extracted and deconstructed +from the graph. For this UCSC track, the decomposed VCF was parsed, +filtered to alt alleles with ≥50 bp REF/ALT length difference, and +merged per snarl site. See the build documentation in the kent source +tree at src/hg/makeDb/doc/hg38/lrSv.txt for details.
+ +The data can be explored interactively with the +Table Browser or +Data Integrator, and accessed from +scripts via our API +(track=aprSv).
+ +For automated download, the bigBed files are at + +http://hgdownload.soe.ucsc.edu/gbdb/hs1/lrSv/apr.bb (native) and + +http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/apr.bb (lifted).
+ ++The original APR pangenome VCF and assemblies can be downloaded from + +https://www.mbru.ac.ae/the-arab-pangenome-reference/, +and the project source code is at + +https://github.com/muddinmbru/arab_pangenome_reference.
+ +Thanks to the Arabic Pangenome Reference team at Mohammed Bin Rashid +University (Dubai), led by Mohammed Uddin, for producing and releasing +the pangenome and its variant calls.
+ ++Nassir N, Almarri MA, Kumail M, Mohamed N, Balan B, Hanif S, AlObathani M, Jamalalail B, Elsokary H, +Kondaramage D et al. + +A draft UAE-based Arab pangenome reference. +Nat Commun. 2025 Jul 24;16(1):6747. +PMID: 40707445; PMC: PMC12290100 +
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