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/meiEul1db.as src/hg/makeDb/scripts/mei/meiEul1db.as
new file mode 100644
index 00000000000..4ce4f20c3f9
--- /dev/null
+++ src/hg/makeDb/scripts/mei/meiEul1db.as
@@ -0,0 +1,32 @@
+table meiEul1db
+"euL1db: curated L1-HS retrotransposon insertion polymorphisms (Mir et al. 2015)"
+(
+string  chrom;            "Reference chromosome"
+uint    chromStart;       "0-based start of MRIP region"
+uint    chromEnd;         "Half-open end of MRIP region"
+string  name;             "MRIP accession (mripN)"
+uint    score;            "Score (pseudo-allele-frequency * 1000)"
+char[1] strand;           "Strand"
+uint    thickStart;       "Start of thick drawing region"
+uint    thickEnd;         "End of thick drawing region"
+uint    itemRgb;          "RGB color, by lineage (germline/somatic/mixed)"
+float   pseudoAlleleFreq; "Pseudo-allele frequency|Aggregated frequency reported by euL1db"
+int     sripCount;        "Sample observations (SRIPs)|Number of sample-level SRIP entries merged into this MRIP"
+int     sampleCount;      "Distinct samples|Number of unique samples contributing"
+int     individualCount;  "Distinct individuals|Number of unique individuals contributing"
+int     studyCount;       "Distinct studies|Number of studies reporting this insertion"
+string  subGroups;        "L1HS sub-group(s)|Comma-separated set (L1-Ta, L1-pre-Ta, L1-Hybrid, unknown)"
+string  integrity;        "Integrity|Comma-separated set (full-length, 5prime-truncated, unknown)"
+string  lineage;          "Lineage|germline, somatic, or both"
+string  pcrValidated;     "PCR validated|yes if any contributing SRIP has PCR evidence"
+string  gene;             "Overlapping gene|Reported in euL1db MRIP table"
+string  inReferenceL1HS;  "In reference L1HS|yes if euL1db marks this MRIP as present in reference"
+string  warning;          "Warning|euL1db curation warning, if any"
+lstring studies;          "Study list|Comma-separated study IDs"
+lstring pmids;            "PubMed IDs|Comma-separated PMIDs"
+lstring methods;          "Detection methods|Comma-separated method names"
+lstring tissues;          "Tissues|Comma-separated unique tissues"
+lstring diseases;         "Clinical conditions|Comma-separated unique disease/clinical states"
+lstring populations;      "Populations|Comma-separated unique populations"
+lstring sampleTable;      "Contributing samples|HTML table (sample, individual, study, lineage, integrity, subgroup, PCR)"
+)