c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 lrnassar Sat Jun 13 09:33:29 2026 -0700 lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258 Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished / do-not-release-yet subtracks stay on dev/alpha and do not graduate with the supertrack (both are already excluded from the lrSvAll merge via databases.tsv). Trim three longLabels to the 85-char limit: hprc2v21Sv, hprc2JasmineSv, and lrSv1kLin. lrSv.html: add the missing "Available Datasets" prose blurbs for Arab APR and CPC so all 15 datasets have a paragraph (was table-row-only). diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index 803d8904725..4b396be3b91 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -312,30 +312,49 @@ inversions) called from phased de novo assemblies with PAV, with per-variant 1000 Genomes population allele frequencies (insertions and deletions) and rich structural/gene annotations. An earlier HGSVC release complementary to HGSVC3.
Structural variants from 65 diverse individuals sequenced and de novo assembled by the Human Genome Structural Variation Consortium phase 3 (HGSVC3). ~177k haplotype-resolved SVs (deletions, insertions and inversions) called with PAV and cross-validated with ten additional callers, with per-site carrier haplotype lists and structural annotations.
++Structural variants from the Arab Pangenome Reference (APR), a +haplotype-resolved pangenome graph built from 53 UAE-resident Arab individuals +drawn from eight countries (PacBio HiFi + ultralong ONT + Hi-C; Nassir et al. +2025). ~73k SVs on hg38 (deletions, insertions, complex and mixed snarls), +lifted from the native T2T-CHM13 assembly; the hs1 track uses the native +coordinates. +
+ ++Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples +spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. +2023). This track shows the CPC contribution to the joint CPC+HPRC graph with +HPRC-specific SVs removed. ~36k SVs on hg38 (deletions, insertions and mixed +snarls), lifted from the native T2T-CHM13 assembly; the hs1 track is native. +
+Structural variants from 100 post-mortem brain samples (Parkinson's disease, incidental Lewy body disease, and healthy controls) sequenced with PacBio HiFi long reads. ~75k high-confidence SVs (deletions, insertions, duplications, inversions) with per-cohort allele frequencies and case-control carrier-rate differentials, from Kim et al. 2026.
Structural variants from 101 long-read whole-genome sequences released alongside the GWAS SVatalog tool (Chirmade et al. 2026). The samples come from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT), a cystic-fibrosis (CF) patient cohort assembled to model patient-specific