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/trackDb/human/swefreq.html src/hg/makeDb/trackDb/human/swefreq.html
index 965b6219283..1fdb2686bd9 100644
--- src/hg/makeDb/trackDb/human/swefreq.html
+++ src/hg/makeDb/trackDb/human/swefreq.html
@@ -1,27 +1,33 @@
 <h2>Description</h2>
 <p>
 <a href="https://swefreq.nbis.se/dataset/SweGen" target="_blank">SweGen</a> provides
 whole-genome sequencing variant frequencies for 1,000 Swedish individuals.
 The 1,000 individuals represent a cross-section of the Swedish population and no disease
 information was used for the selection. The frequency data may therefore include genetic variants
 that are associated with, or causative of, disease. SweGen also provides SV calls, TEs, MELT
 results for TEs, HLAs and a FASTA file with new sequence not in hg38. There is
 also a version for the T2T CHM13 assembly.  The full dataset can be browsed at
 the
 <a href="https://swefreq.nbis.se/dataset/SweGen/browser" target="_blank">SweGen Browser</a>.
 </p>
+<p>
+The mobile element insertions called by MELT on the same 1,000 SweGen
+samples are loaded as a separate track,
+<a href="hgTrackUi?g=meiSwegen">SweGen 1000 MEIs</a>, in the
+<a href="hgTrackUi?g=mei">Mobile Element Insertions</a> collection.
+</p>
 
 <h2>Data Access</h2>
 <p>
 Due to license restrictions, the data for this track cannot be downloaded from the UCSC
 Genome Browser. The Table Browser, Data Integrator, and download server are not available
 for this track.
 </p>
 <p>
 VCF files can be requested at
 <a href="https://swefreq.nbis.se/dataset/SweGen" target="_blank">SweGen</a> via a form. The request
 needs manual approval, which usually is quick. If there is no reply, email SweGen directly.
 </p>
 
 <h2>Methods</h2>
 <p>