c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 lrnassar Sat Jun 13 09:33:29 2026 -0700 lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258 Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished / do-not-release-yet subtracks stay on dev/alpha and do not graduate with the supertrack (both are already excluded from the lrSvAll merge via databases.tsv).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.

HGSVC3 65 SVs

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.

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Arab APR 53 SVs

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+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. +

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CPC 58 SVs

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+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. +

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Kim PD Brain SVs

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.

SVatalog 101 SVs

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