4f8f8773bec66a9e993e9897e0b032c6e97dead8
max
  Fri May 15 10:12:29 2026 -0700
mei: add HMEID, SweGen, and euL1db subtracks

Three new MEI catalogues under the existing mei superTrack:

meiHmeid     (hg38)        36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP,
5,675 individuals, Niu et al. 2022, PMID 35212372).
Site-level VCF; per-cohort and per-1KGP super-
population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK.

meiSwegen    (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample
Swedish cohort (Ameur 2017, PMID 28832569;
Gardner 2017, PMID 28855259). Built on hg19,
liftOver to hg38 (10 unmapped). tableBrowser off
per SweGen distribution terms.

meiEul1db   (hg19+hg38)    8,988 curated L1-HS insertion polymorphisms
(MRIPs) from euL1db v1.00 (Mir 2015, PMID
25352549), aggregating 142,495 sample-level
SRIPs across 32 published studies. Coloured by
lineage (germline/somatic/mixed). Built on hg19,
liftOver to hg38 (3 unmapped). Helman2014 used
numeric chrom names (23=X, 24=Y) which are
renamed during the build.

meiEul1dbRef (hg19+hg38)   1,540 reference-genome L1-HS copies catalogued
by euL1db (companion to meiEul1db).

Single shared mei.ra (in human/) uses $D substitution so each stanza
serves both assemblies where applicable.

refs #37524

diff --git src/hg/makeDb/scripts/mei/meiSwegen.as src/hg/makeDb/scripts/mei/meiSwegen.as
new file mode 100644
index 00000000000..7b008cc2d69
--- /dev/null
+++ src/hg/makeDb/scripts/mei/meiSwegen.as
@@ -0,0 +1,22 @@
+table meiSwegen
+"Mobile Element Insertions in 1,000 SweGen samples (MELT, lifted from GRCh37 to GRCh38)"
+(
+string  chrom;             "Reference chromosome or scaffold"
+uint    chromStart;        "0-based start position (anchor base)"
+uint    chromEnd;          "Half-open end position (anchor base + 1)"
+string  name;              "Item label (MEI class, allele count)"
+uint    score;             "Score (alt-allele frequency * 1000)"
+char[1] strand;            "Strand (always .)"
+uint    thickStart;        "Start of thick drawing region"
+uint    thickEnd;          "End of thick drawing region"
+uint    itemRgb;           "RGB color, by mobile-element class"
+string  teClass;           "TE class|Family of mobile element (Alu, L1, SVA, HERVK)"
+int     svLen;             "Insertion length (bp), -1 if unknown"
+string  meiSubfamily;      "MELT MEI subfamily|MELT MEIINFO NAME (e.g. AluYa5, L1Ta, SVA, HERVK)"
+string  tsd;               "Target site duplication|TSD sequence reported by MELT, '.' if unknown"
+int     assess;            "MELT ASSESS score|0=no overlapping reads, 1=imprecise, 2=discordant pairs only, 3=left-side TSD only, 4=right-side TSD only, 5=TSD decided with split reads (highest quality)"
+string  internalGene;      "Gene context|Transcript and location if insertion is in or near a gene (MELT INTERNAL); empty otherwise"
+int     altAlleleCount;    "Carrier haplotypes|Haplotypes carrying the insertion (MELT_AN field, actually allele count)"
+float   altAlleleFreq;     "Allele frequency|Alt-allele frequency across the 1,000 SweGen samples (MELT_AF)"
+string  filterStatus;      "MELT filter|VCF FILTER column: PASS, hDP, rSD, s25 (or combinations)"
+)