People running their own copy of the Genome Browser ask us three questions often enough that it is worth answering them in one place: which tracks we are not allowed to pass on, which tracks change on their own, and which tracks were built by someone other than UCSC. This page is rebuilt automatically, so it reflects the current state of our servers rather than a hand-kept list.
For installation instructions see the mirror documentation. Questions are welcome on the genome-mirror mailing list.
These tracks reach us under terms that let us display the data but not pass it on. You can see them on our site, and in most cases you can obtain the same data yourself directly from the group that produced it, but we cannot include them in a mirror or on our download server. The reasons vary: some are commercial licenses, others are consent agreements attached to human cohorts. Check the description page of an individual track for who to approach about access.
| Track | Table or track name | Assemblies |
|---|---|---|
| COSMIC Regions | cosmicRegions |
hg19 hg38 |
| DECIPHER CNVs | decipher |
hg19 hg38 |
| DECIPHER SNVs | decipherSnvs |
hg19 hg38 |
| AlphaGenome | alphaGenome |
hg38 |
| Mutation: A | alphaGenomeA |
hg38 |
| Mutation: C | alphaGenomeC |
hg38 |
| Mutation: G | alphaGenomeG |
hg38 |
| Mutation: T | alphaGenomeT |
hg38 |
| PrimateAI-3D | primateAi |
hg19 hg38 |
| PromoterAI | promoterAi |
hg38 |
| HGMD Public 2025 | hgmd |
hg19 hg38 |
| LOVD Variants | lovdComp |
hg19 hg38 |
| Nextstrain Mutations | nextstrainSamples |
wuhCor1 |
| OMIM Alleles | omimAvSnp |
hg18 hg19 hg38 |
| OMIM Cyto Loci | omimLocation |
hg18 hg19 hg38 |
| OMIM Genes | omimGene2 |
hg18 hg19 hg38 |
| Phylogeny: GISAID | sarsCov2Phylo |
wuhCor1 |
| SpliceAI Variants | spliceAI |
hg19 hg38 |
| SpliceAI indels | spliceAIindels |
hg19 hg38 |
| SpliceAI indels (masked) | spliceAIindelsMasked |
hg19 hg38 |
| SpliceAI SNVs | spliceAIsnvs |
hg19 hg38 |
| SpliceAI SNVs (masked) | spliceAIsnvsMasked |
hg19 hg38 |
The 18 tracks below are also restricted, and are listed apart from the rest only because there are so many of them. Each is allele frequencies from one sequencing cohort, usually a national project, and each carries its own agreement with the group that collected the samples. Almost all of them are aggregate frequencies rather than individual genotypes, but that does not make them ours to pass on.
| Track | Table or track name | Assemblies |
|---|---|---|
| Mexico Biobank, 6k Array | mexbb |
hg19 hg38 |
| 12 Afr Pops 180 WGS | tishkoff180 |
hg38 |
| AllOfUs v7 245k WGS | allofus |
hg38 |
| Australia MGRB 4k WGS | mgrb |
hg38 |
| China ChinaMAP 10.5k WGS | chinamap |
hg38 |
| FinnGen R12 500k imputed | finngen |
hg38 |
| India GenomeIndia 9.7k WGS | genomeindia |
hg38 |
| Korea KOVA 5.3k mixed | kova |
hg38 |
| Mexico Biobank 6k Array | mxbFreq |
hg38 |
| NHLBI TOPMed 10 151k WGS | topmed |
hg38 |
| SFARI SPARK 12k WGS | sfariSparkWgs |
hg38 |
| SFARI SPARK 140k WES | sfariSparkExomes |
hg38 |
| Singapore NPM 9.7k WGS | npm |
hg38 |
| SNV Frequencies: Disease cohorts | varFreqsAffected |
hg38 |
| SNV Frequencies: Genotyping Array Databases Combined | varFreqsArray |
hg38 |
| SNV Frequencies: Population reference | varFreqsBackground |
hg38 |
| Sweden SweGen 1k WGS | swefreq |
hg38 |
| Taiwan TPMI Axiom array | tpmi |
hg38 |
A track appears in one of the two tables above if any of three things is true of
it: its configuration says
tableBrowser off; its noGenomeReason refers to distribution
terms, which is how OMIM is marked and is missed by a search for the first setting
alone; or its table exists on our servers but is deliberately absent from the download
server. No single one of those catches everything, so all three are checked. Note that
some tracks are withheld from whole-genome Table Browser queries only because they are
too large to return, not for any licensing reason, and those are not listed above.
Every track named above is cross-checked against the download server each time this page is rebuilt. Any file that turns out to be reachable there is reported to us privately rather than named on this page.
These tracks are rebuilt on a schedule without anyone at UCSC touching them. If you mirror them, your copy will drift from ours until you synchronize again. Times are US Pacific.
| Source | Updated | Tracks affected | Assemblies |
|---|---|---|---|
| CIViC | monthly on day 2 at 12:12 | CIViC | 2 |
| ClinGen | daily at 09:00 | ClinGen; ClinGen Haploinsufficiency; ClinGen Triplosensitivity; ClinGen VCEP Specifications; ClinGen Validity | 2 |
| ClinGen CSpec | weekly (Wed) at 11:11 | ClinGen VCEP Specifications | 2 |
| ClinVar | monthly on day 8 at 00:08 | ClinVar CNVs; ClinVar SNVs; ClinVar Variants; ClinVar interp | 2 |
| dbVar | monthly on day 2 at 08:13 | dbVar Common SV; dbVar Conflict SV; dbVar Curated 1000 Genomes SVs; dbVar Curated Abel SVs; dbVar Curated African SVs; dbVar Curated All Populations; dbVar Curated American SVs; dbVar Curated Byrska-Bishop SVs; dbVar Curated Conflict SVs; dbVar Curated DECIPHER SVs; dbVar Curated East Asian SVs; dbVar Curated European SVs; dbVar Curated Lee SVs; dbVar Curated Other Pop SVs; dbVar Curated South Asian SVs; dbVar Curated gnomAD SVs; dbVar Healthy SVs; dbVar Other SV; dbVar Phenotype SVs; dbVar Somatic SV; dbVar Somatic SVs | 2 |
| DECIPHER | daily at 04:11 | DECIPHER; DECIPHER CNVs; DECIPHER Population CNVs; DECIPHER SNVs | 1 |
| GenCC | weekly (Tue) at 16:08 | GenCC | 2 |
| Gene2Phenotype | monthly on day 5 at 06:22 | G2P Project | 2 |
| GeneReviews | weekly (Tue) at 08:00 | GeneReviews | 3 |
| GRC Incident | daily at 06:33 | GRC Incident | 10 |
| GWAS Catalog | weekly (Wed) at 04:41 | GWAS Catalog | 3 |
| InSiGHT VCEP ClinVar | weekly (Tue) at 03:08 | updates a hub rather than a trackDb track: insightClinVar and pms2clParalogVars, on hg19 and hg38 | 2 |
| LOVD | weekly (Mon) at 13:14 | LOVD Variants; LOVD Variants < 50 bp + ins; LOVD Variants >= 50 bp | 2 |
| MalaCards | monthly on day 20 at 04:04 | loads the hg38 malacards table; no track shows it, but the gene details page uses it for the MalaCards disease links | 1 |
| MANE | weekly (Mon) at 05:11 | MANE | 1 |
| MITOMAP | weekly (Wed) at 08:55 | MITOMAP; MITOMAP Disease Muts; MITOMAP Variants | 2 |
| NCBI RefSeq | weekly (Wed) at 08:23 | RefSeq Alignments; RefSeq All; RefSeq Curated; RefSeq Diffs; RefSeq HGMD; RefSeq Historical; RefSeq Other; RefSeq Predicted; RefSeq Select; RefSeq Select and MANE | 4 |
| OMIM | daily at 04:17 | OMIM; OMIM Alleles; OMIM Cyto Loci; OMIM Genes | 3 |
| Orphanet | monthly on day 10 at 07:10 | Orphanet | 2 |
| PanelApp | weekly (Tue) at 10:10 | PanelApp; PanelApp Australia CNVs; PanelApp Australia Genes; PanelApp Australia STRs; PanelApp GE CNVs; PanelApp GE Genes; PanelApp GE STRs | 2 |
| PubTator | daily at 08:28 | PubTator Variants | 2 |
| STRchive | weekly (Mon) at 07:45 | STRchive | 3 |
| UniProt | monthly on day 26 at 07:00 | Mutations; UniProt | 123 |
| UniProt (wuhCor1) | daily at 04:00 | UniProt; Mutations on wuhCor1 | 1 |
| VarChat | weekly (Thu) at 22:22 | enGenome VarChat | 2 |
| VISTA Enhancers | monthly on day 1 at 09:00 | VISTA Enhancers | 2 |
These watch for new releases upstream and send us mail. They update nothing on their own, and are listed so that the schedule above is not mistaken for the whole picture.
| Check | Runs | What it looks at |
|---|---|---|
| RefSeq Historical | weekly (Wed) at 08:40 | checks whether NCBI has a new release; changes no data |
| VCEP spec versions | monthly on day 15 at 06:40 | compares our VCEP pages against the ClinGen registry |
Some assemblies in our GenArk collection carry annotation built by outside groups rather than by UCSC. The data sits alongside our own tracks, but the group named below produced it, and questions about the underlying annotation are best sent to that group.
| Contributing group | Assemblies |
|---|---|
| tiberius | 2259 |
| TOGAv2 | 557 |
| hprc2annot | 462 |
| VEuPathDB | 442 |
| HPRCv2 | 440 |
| evaSnp8 | 117 |
| vgp577way | 21 |
| lowelab | 18 |
| RCPediaVGP_v1 | 5 |
| evaSnp9 | 3 |
| T2T-marmoset | 2 |
| T2TPrimates | 2 |
| bTaeGut7 | 1 |
| vgp577chain | 1 |
| TOGA | 1 |
4331 assemblies carry contributed annotation, from 15 groups.
This page was generated on 2026-10-01 from the current state of our servers.