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/meiEul1dbRef.as src/hg/makeDb/scripts/mei/meiEul1dbRef.as
new file mode 100644
index 00000000000..7569ab67e94
--- /dev/null
+++ src/hg/makeDb/scripts/mei/meiEul1dbRef.as
@@ -0,0 +1,19 @@
+table meiEul1dbRef
+"euL1db: L1-HS copies present in the human reference genome"
+(
+string  chrom;        "Reference chromosome"
+uint    chromStart;   "0-based start of reference L1HS element"
+uint    chromEnd;     "Half-open end of reference L1HS element"
+string  name;         "Subgroup label (L1HS-Ta, L1HS-PreTa, L1HS-Hybrid)"
+uint    score;        "Score (unused, 0)"
+char[1] strand;       "Strand"
+uint    thickStart;   "Start of thick drawing region"
+uint    thickEnd;     "End of thick drawing region"
+uint    itemRgb;      "RGB color, by L1HS subgroup"
+string  family;       "Family|Always L1HS"
+string  subGroup;     "Sub-group|L1HS-Ta, L1HS-PreTa, L1HS-Hybrid"
+string  integrity;    "Integrity|full-length or 5prime-truncated"
+uint    refStart;     "Position on L1HS consensus|5' start in L1HS consensus sequence"
+uint    refStop;      "Position on L1HS consensus|3' stop in L1HS consensus sequence"
+uint    elementLen;   "Element length (bp)"
+)