3bf9e1a841206d3bf5902e06791ef5be2dbdbd39
max
  Fri Jul 17 09:09:47 2026 -0700
lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv)

#Preview2 week - bugs introduced now will need a build patch to fix
888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with
per-superpopulation allele frequencies, imputation-accuracy metrics and UK
Biobank SV-WAS associations. Converter approximates AC/AN from AF and the
genotype missing rate (source has no allele count), stores BND mate breakends,
and follows the shared lrSv svType/svLen/insLen/AC field convention so the
container-level filters apply. refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvNoyvert.as src/hg/makeDb/scripts/lrSv/lrSvNoyvert.as
new file mode 100644
index 00000000000..f6d8752ec7e
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvNoyvert.as
@@ -0,0 +1,35 @@
+table lrSvNoyvert
+"Multi-ancestry long-read structural variants (888 samples, Noyvert et al. 2025)"
+    (
+    string chrom;              "Chromosome"
+    uint chromStart;           "Start position"
+    uint chromEnd;             "End position"
+    string name;               "Variant name"
+    uint score;                "Score"
+    char[1] strand;            "Strand"
+    uint thickStart;           "Thick start (same as chromStart)"
+    uint thickEnd;             "Thick end (same as chromEnd)"
+    uint reserved;             "Item color"
+    string svType;             "SV Type|DEL, INS, INV, DUP or BND"
+    int svLen;                 "SV Length|Length of the variant on the reference in base pairs"
+    int insLen;                "Insertion Length|Length of inserted sequence, 0 for non-insertions"
+    int AC;                    "Allele Count|Approximate alternate allele count (AF times allele number)"
+    int AN;                    "Allele Number|Approximate called alleles, 2 x 888 x (1 - missing rate)"
+    float AF;                  "Allele Frequency|Overall allele frequency across all samples"
+    float afAfr;               "AF African|Allele frequency in African samples (n=241)"
+    float afAmr;               "AF Admixed American|Allele frequency in Admixed American samples (n=144)"
+    float afEas;               "AF East Asian|Allele frequency in East Asian samples (n=168)"
+    float afEur;               "AF European|Allele frequency in European samples (n=164)"
+    float afSas;               "AF South Asian|Allele frequency in South Asian samples (n=171)"
+    string secondBp;           "Second Breakpoint|Mate breakend locus and orientation, BND records only"
+    float stdevLen;            "Length StdDev|Sniffles2 standard deviation of SV length across samples"
+    float stdevPos;            "Position StdDev|Sniffles2 standard deviation of the breakpoint position"
+    float missingRate;         "Genotype Missing Rate|Fraction of samples with a missing genotype"
+    string hwe;                "HWE p-values|Hardy-Weinberg exact test p-value per superpopulation"
+    float r2Loo;               "Imputation r2 (LOO)|Leave-one-out internal imputation accuracy"
+    float concordanceLoo;      "Minor Allele Concordance (LOO)|Leave-one-out minor-allele genotype concordance"
+    float afUkb;               "AF in UK Biobank|Imputed allele frequency in the UK Biobank cohort"
+    float r2Ukb;               "Imputation r2 (UKB)|Imputation accuracy in the UK Biobank cohort"
+    int nGwas;                 "GWAS Hit Count|Number of significant UK Biobank SV-WAS trait associations"
+    lstring ukbGwas;           "UK Biobank GWAS|Significant SV-WAS associations (trait: info, log10 p-value)"
+    )