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 @@ -1,78 +1,90 @@ <h2>Description</h2> <p> This track collection shows <b>Mobile Element Insertions (MEIs)</b> in the human genome. Mobile elements are stretches of DNA that have copied themselves into new genomic locations during evolution, and a few families remain active enough to keep producing new insertions in the human population today. The three element classes responsible for almost all MEIs in humans are <b>Alu</b> (~300 bp SINE retrotransposons), <b>L1/LINE-1</b> (typically 6 kb autonomous retrotransposons) and <b>SVA</b> (composite elements of ~700-3000 bp). Polymorphic MEIs - sites where some individuals carry the inserted element while others do not - are an important source of structural variation, can disrupt or alter gene expression, and have been implicated in a number of human diseases. </p> <p> 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> <ul> <li><span style="display:inline-block;background-color:#0072B2;width:18px;height:12px;vertical-align:middle;"></span> <b>Alu</b> — SINE (Short INterspersed Element)</li> <li><span style="display:inline-block;background-color:#D55E00;width:18px;height:12px;vertical-align:middle;"></span> <b>L1</b> — LINE-1 (Long INterspersed Element-1)</li> <li><span style="display:inline-block;background-color:#009E73;width:18px;height:12px;vertical-align:middle;"></span> <b>SVA</b> (SINE-VNTR-Alu) — composite retrotransposon</li> <li><span style="display:inline-block;background-color:#CC79A7;width:18px;height:12px;vertical-align:middle;"></span> <b>HERVK</b> (Human Endogenous Retrovirus K) — endogenous retrovirus</li> <li><span style="display:inline-block;background-color:#000000;width:18px;height:12px;vertical-align:middle;"></span> <b>snRNA</b> — small nuclear RNA</li> </ul> <p> Filters available on the subtrack configuration page allow restricting the displayed items by element class, insertion length, allele frequency, number of carrier samples, the number of MEI callers that supported the call, validation by L1ME-AID or PALMER, and overlap with reference segmental duplications and tandem repeats. </p> <h2>Data Access</h2> <p> Each subtrack has its own description page with details on file location, the autoSql schema, citation and download instructions. </p> <h2>References</h2> <p> Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D <em>et al</em>. <a href="https://doi.org/10.1038/s41586-025-09140-6" target="_blank"> Complex genetic variation in nearly complete human genomes</a>. <em>Nature</em>. 2025 Aug;644(8076):430-441. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank">40702183</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350169/" target="_blank">PMC12350169</a> </p>