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These tracks are useful in combination with the variants track for evaluating new transcript models. They can be used to assess potential exon boundaries or possible splice acceptor sites.
We would like to thank Illumina for making SpliceAI available, both the model and the precomputed data files. Thanks to Francois Lecoquierre from the University of Oxford, Jean-Madeleine de Sainte Agathe from Institut Pasteur Paris, and Michael Hiller from the Senckenberg Museum Frankfurt for suggesting and then creating the SpliceAI Wildtype annotations. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.
We are happy to announce the release of the Panmask Easy 151b Regions track for hg38. This new track is available in the Problematic Regions superTrack. The track contains a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. Easy regions are derived for variant filtration agnostic to individual samples. They are genomic intervals where general variant callers achieve high accuracy without sophisticated filtering.
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The pm151 regions are used to filter spurious variant calls in centromeres, long repeats, and other genomic regions where short-read mapping is often problematic. They cover 88.2% of hg38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. The track can be used to filter variant calls for clinical or research human samples. It shows regions that are easy to sequence, rather than those that are problematic. The data was derived from the HPRC assemblies, and this track presents the 151b-easy panmask set.
We would like to thank Heng Li's group at Harvard Medical School for making this data available. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.
Each track includes allele frequency and sample count annotations, with additional filtering options for variant size and type. Users can click on individual variants to view detailed metadata, such as allele counts, homozygous/heterozygous call distributions, and Hardy-Weinberg equilibrium values.
We would like to thank Mike Schatz, Evan Eichler, and all CoLoRSdb investigators for generating and making the data publicly available. We would also like to thank Karen Wang and Jairo Navarro Gonzalez for the creation and release of these tracks.
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We would like to thank the G2P project for making this data publicly available. We would also like to thank Jaidan Jenkins-Kiefer and Jairo Navarro Gonzalez for the creation and release of the Genome Browser tracks.
We are excited to announce the release of the MaveDB Experiment Heatmaps and Alignment track for hg38. This release provides heatmaps of multiplexed assays of variant effects (MAVE) from MaveDB. Each heatmap presents the results of an experiment where many small substitutions were tested within a gene to examine their functional consequences. Accompanying tracks display alignments of each experiment sequence to the genome.
Please note that only a subset of MaveDB experiments could be displayed as heatmaps; the sequence alignments in this track only cover those experiments.
Hover over each item in the heatmap to see the consequence of substituting individual amino acids within the genome with alternatives. Score ranges vary among experiments, but each is presented with the highest scores in red, the lowest scores in blue, and scores at the midpoint between the two in silver. Higher scores correspond to a higher enrichment level for that variant compared to others in the experiment set.
We would like to thank Jeremy Arbesfeld and the MaveDB team for making this data publicly available. We would also like to thank Melissa Cline, Jonathan Casper, and Jairo Navarro for the @@ -1234,31 +1234,31 @@
We are pleased to announce the release of the ENCODE4 long-read RNA-seq transcripts track for hg38 and mm10. This track annotates transcripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This is presented alongside sample enrichment information to show how promoter selection, splice pattern, and 3’ processing are deployed across human tissues.
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Transcripts are labeled with triplets, e.g. [1,1,1] or [1,1,3] or [2,1,3]. If transcripts share a number in any of the positions that means they share that feature, e.g. sharing a 8 in the second position but different numbers in the others means those two transcripts share the same set of exons, but different start and end sites.
This track is part of a "Long-read Transcripts" supertrack that will consist of other datasets derived from third-generation sequencing technology, such as PacBio and Oxford Nanopore.
@@ -1713,31 +1713,31 @@ expression levels across 50 tissues from the Genotype Tissue Expression (GTEx) v10 dataset, showing a comprehensive view of the expression of exons across a gene using the proportion expression across transcripts, or pext metric, a transcript-level annotation metric which quantifies isoform expression for variants.This is especially useful for those interested in alternative splicing and clinical assessment of variants. For more information, see the track description page and the associated publication.
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We would like to thank the gnomAD team and the UCSC Genome Browser team members Jeltje van Baren, Max Haeussler, Lou Nassar, and Anna Benet-Pages for developing and releasing this track, as well as making the Exon Relevance RTS.
We are happy to announce an update to the VISTA Enhancers tracks for human
(GRCh38/hg38
and
The example above uses the
In this final example, the Items in the NCBI RefSeq Historical track for hg38 have all items that begin with
"NM" highlighted in red.
We would like to thank Chris Lee and Jairo Navarro for their efforts in creating and testing the
highlight feature for track hubs.
We are happy to announce the release of the enGenome VarChat track for the
hg38/GRCh38
and hg19/GRCh37 human assemblies,
available in the Variants in Papers superTrack.
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href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project
highlightText.name NM*
highlightText setting, which will apply a highlight on the
field name. Using this setting, any items that begin with NM are
highlighted.
highlightColor #ff0000
highlightColor is used to set the default highlight color.
With this setting, all highlight stripes will use the color red, #ff0000.
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Feb. 24, 2025 enGenome VarChat track for human (hg38 and hg19)
The Genome Browser already provided single-cell RNA-seq datasets for the human GRCh38/hg38 assembly, but those data have so far been split among a collection of tracks depending on the organ and publication source. We are happy to announce that data from 12 of those papers (and 14 organs) are now available in a combined Merged Cells track that provides normalized RNA-seq values for every cell type in those sets. All components were normalized to show expression in parts per million.
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The following tracks were incorporated into this Merged Cells track:
We are pleased to release a new track, ClinVar Interpretations, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the ClinVar Composite. It is the first track to use our bead graph display, which is a variation of our existing lollipop display.
The ClinVar Interpretations track displays the genomic positions of individual variant submissions and interpretations of the clinical significance, as well as their relationship to disease in the ClinVar database. As seen on the image below, the variants are classified into six categories each on a separate horizontal line:
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The size of the bead on the line represents the number of submissions at that genomic position. The color of the beads aids to distinguish the categories further. Hovering on the track items shows the genomic variations which start at that position and the number of individual submissions with that classification. Additional information on the variants @@ -8362,59 +8362,59 @@ Lastly, multiple feature options have been added to both tracks independently:
Below is an example of the filter options available for the ClinVar SNVs track. For additional details on the updated display, see the track description page.
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We have created a new composite track, ClinGen, and deprecated the previous ClinGen CNVs track. The ClinGen CNVs track will continue to be available, however, the data will no longer be updated. This was done by request of ClinGen, as all the data, as well as further updates, can be found in the ClinVar Copy Number Variants (ClinVar CNVs) track.
The new ClinGen composite track includes three new tracks described below:
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For more information on these tracks, including display conventions, scores, and classifications, see the track description page.
We would like to thank Erin Riggs and May Flowers as well as the rest of the ClinGen team. We would also like to thank ClinVar for making these data available. Track development and release was made possible by Anna Benet-Pages, Christopher Lee, Max Haeussler, and Lou Nassar.
@@ -9664,31 +9664,31 @@ Control Only SV's - gnomAD Structural Variants Controls Only
These data can be found as part of the gnomAD super-track. More information on this track can be found in the track description pages, as well as the gnomAD site.
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We would like to thank the Genome Aggregation Database Consortium for making these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks.
We have released a new video to the Browser's hg38.
We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role creating, documenting, and reviewing these tracks.
We are pleased to announce a new track, Avada Variants, now available on hg19. Additionally, we have updated the Mastermind Variants track and expanded it to hg38.
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The Avada Variants track shows the genomic positions of variants in the AVADA database. AVADA is a database of variants built by machine learning software that analyzes full text research articles in PDF format to find genes and variants that look most relevant for genetic diagnosis.
Additional information can be found on the AVADA publication.
The Mastermind Variants track is now available for the hg38 assembly @@ -17391,31 +17391,31 @@ modifications suggestive of enhancer and promoter activity, DNAse clusters indicating open chromatin, regions of transcription factor binding, and transcription levels. When viewed in combination, the complementary nature of the data within these tracks has the potential to greatly facilitate our understanding of regulatory DNA.
The data comprising these tracks were generated from hundreds of experiments on multiple cell lines conducted by labs participating in the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to the UCSC ENCODE Data Coordination Center for display on the Genome Browser.
Faced with the problem of how to display such a large amount of data in a manner facilitating analysis, UCSC has developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen. Each of the cell lines in a track is associated with a particular color. Light, saturated colors are used to produce the best transparent overlay.
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The data in the ENCODE Regulation super-track, as with all data from the production phase of the ENCODE project, have genome-wide coverage. In general, Genome Browser tracks that show ENCODE-generated data can be identified by the double-helix icon preceding the name in the track list. Currently, the ENCODE Regulation data are available only on the Mar. 2006 (NCBI Build 36, UCSC version hg18) assembly of the human genome.
For a detailed description of the datasets contained in this super-track and a discussion of how the tracks can be used synergistically to examine regions of regulatory functionality within the genome, see the track description page.
We have released a Genome Browser for the latest assembly of Cat (Felis catus). The GTB @@ -17478,31 +17478,31 @@ We are pleased to announce the release of a new Conservation track based on the zebrafish (danRer6) assembly. This track shows multiple alignments of 6 vertebrate species and measurements of evolutionary conservation using phastCons from the PHAST package. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are displayed in the companion "Most Conserved" track.
For more details, please visit the track description page.
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| Top graph: total traffic on the UCSC domain during June-July,
2000. Bottom graph: page hit statistics on genome.ucsc.edu in the ensuing years since the Genome
Browser was released. |
UCSC is pleased to celebrate the 10-year anniversary of the debut of the first assembled human genome sequence and its then-fledgling visualization tool, the UCSC Genome Browser. Released on July 7, 2000, the genome sequence instantly created unprecedented web traffic on the ucsc.edu domain as researchers around the world scrambled to download the data: 0.5 terabytes per day, a record that stood for many years.
David Haussler recounts that day: "Seeing the waterfall of As, Gs, Cs, and Ts pouring off our
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