68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa lrnassar Mon Jun 1 14:40:45 2026 -0700 varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642 diff --git src/hg/makeDb/trackDb/human/mei.html src/hg/makeDb/trackDb/human/mei.html index 1f8ba13ecb9..e708a6d62a3 100644 --- src/hg/makeDb/trackDb/human/mei.html +++ src/hg/makeDb/trackDb/human/mei.html @@ -1,90 +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> + <a href="hgTrackUi?g=varFreqs">SNV 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>