00e086afbcb8296c6aef946c13eeb777f34bac02
max
  Mon May 11 07:03:10 2026 -0700
mei: new track for HGSVC3 mobile element insertions on hg38 and hs1

12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon
et al. 2025). Single shared trackDb stanza in human/mei.ra with $D
substitution. Okabe-Ito colors, INS-svLen:carrierCount item names,
inserted DNA in an insertSeq field. Cross-link to lrSv via
relatedTracks.ra. refs #37524

diff --git src/hg/makeDb/scripts/mei/meiHgsvc3.as src/hg/makeDb/scripts/mei/meiHgsvc3.as
new file mode 100644
index 00000000000..b732e266a3f
--- /dev/null
+++ src/hg/makeDb/scripts/mei/meiHgsvc3.as
@@ -0,0 +1,29 @@
+table meiHgsvc3
+"Novel Mobile Element Insertions in 65 HGSVC3 long-read assembled samples (vs 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 (INS, insertion length, carrier sample 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, snRNA)"
+string  teType;            "Repeat designation|Repeat designation as reported in source (e.g. SINE/Alu)"
+int     svLen;             "Insertion length (bp)"
+int     altAlleleCount;    "Carrier haplotypes|Haplotypes carrying the insertion"
+int     alleleNumber;      "Genotyped haplotypes|Total haplotypes successfully genotyped"
+float   altAlleleFreq;     "Allele frequency|Fraction of genotyped haplotypes carrying the insertion"
+int     carrierCount;      "Carrier samples|Samples with at least one insertion allele"
+int     sampleCount;       "Genotyped samples|Samples with at least one called haplotype"
+string  sourceSample;      "Discovery sample|Sample-haplotype in which the insertion was originally called"
+int     callerCount;       "Caller count|Number of MEI callers supporting this insertion (1 or 2)"
+string  l1meAid;           "L1ME-AID validated|Whether the insertion was validated by L1ME-AID (Yes/No)"
+string  palmer;            "PALMER validated|Whether the insertion was validated by PALMER (Yes/No)"
+float   refSegDup;         "Segmental dup. overlap|Fraction of insertion site overlapping reference segmental duplications (REF_SD)"
+string  refTrf;            "Tandem repeat|Insertion site overlaps a reference tandem repeat (REF_TRF)"
+lstring carrierSamples;    "Carrier sample list|Comma-separated list of samples with at least one insertion allele"
+lstring insertSeq;         "Inserted sequence|DNA sequence of the inserted mobile element (ALT allele minus the anchor base)"
+)