6b0d68657267f1e02c47d4224ea62446bbbb2ba0 max Fri May 22 06:55:52 2026 -0700 small non-AI changes to the html docs pages of the long-read SV tracks diff --git src/hg/makeDb/trackDb/human/mei.html src/hg/makeDb/trackDb/human/mei.html index 937ff3d0c63..1f8ba13ecb9 100644 --- src/hg/makeDb/trackDb/human/mei.html +++ src/hg/makeDb/trackDb/human/mei.html @@ -17,30 +17,42 @@ Tracks in this collection report MEI calls assembled from long-read genome sequencing. Items are colored by element class. </p> <h3>Available subtracks</h3> <ul> <li><a href="hgTrackUi?g=meiHgsvc3">HGSVC3 65 MEIs</a> - mobile element insertions identified in 65 diverse long-read assembled samples relative to the reference assembly (HGSVC3, Logsdon et al. 2025, <em>Nature</em>). Available on both GRCh38/hg38 (12,642 MEIs) and T2T-CHM13/hs1 (12,919 MEIs).</li> <li><a href="hgTrackUi?g=meiDeepmei1kg">DeepMEI 1000G MEIs</a> - 91,617 mobile element insertions called by the DeepMEI convolutional neural network on the 3,202 high-coverage 1000 Genomes samples (Xu et al. 2023, bioRxiv). hg38 only.</li> + <li><a href="hgTrackUi?g=meiHmeid">HMEID 5675 MEIs</a> - + 36,699 mobile element insertions called by MELT on 5,675 samples + from the NyuWa Chinese cohort and the 1000 Genomes Project, + with per-cohort and per-super-population allele frequencies + (Niu et al. 2022, <em>Nucleic Acids Res</em>). hg38 only.</li> + <li><a href="hgTrackUi?g=meiSwegen">SweGen 1000 MEIs</a> - + 18,090 mobile element insertions called by MELT v2.0.2 on the + 1,000 SweGen Swedish whole-genome samples (Ameur et al. 2017, + <em>Eur J Hum Genet</em>), lifted from GRCh37 to hg38. The + short-variant frequencies for the same cohort are in the + <a href="hgTrackUi?g=swegen">SweGen</a> subtrack of + <a href="hgTrackUi?g=varFreqs">Variant Frequencies</a>.</li> </ul> <p> Related: <a href="hgTrackUi?g=lrSv">Long-read Structural Variants</a> contains the parent SV callsets from which several of these MEI tracks are derived. <a href="hgTrackUi?g=rmsk">RepeatMasker</a> shows all annotated mobile elements in the reference genome (regardless of whether they are polymorphic). </p> <h2>Display Conventions and Configuration</h2> <p> Each MEI is shown as a 1-bp anchor block at the position where the insertion attaches to the reference. Items are colored by element class: </p>