Snp reference file download ucsc genome browser

Multiple alignments of 4 vertebrate genomes with Medaka Conservation scores for alignments of 4 vertebrate genomes with Medaka. Multiple alignments of 6 vertebrate genomes with the Medium ground finch Conservation scores for alignments of 6 vertebrate genomes with the Medium ground finch Basewise conservation scores phyloP of 6 vertebrate genomes with the Medium ground finch.

Multiple alignments of 59 vertebrate genomes with Mouse Conservation scores for alignments of 59 vertebrate genomes with Mouse Basewise conservation scores phyloP of 59 vertebrate genomes with Mouse FASTA alignments of 59 vertebrate genomes with Mouse for CDS regions. GRCm38 Patch 6 - Sequence files. Multiple alignments of 29 vertebrate genomes with Mouse Conservation scores for alignments of 29 vertebrate genomes with Mouse Basewise conservation scores phyloP of 29 vertebrate genomes with Mouse FASTA alignments of 29 vertebrate genomes with Mouse for CDS regions.

Multiple alignments of 16 vertebrate genomes with Mouse Conservation scores for alignments of 16 vertebrate genomes with Mouse.

Multiple alignments of 9 vertebrate genomes with Mouse Conservation scores for alignments of 9 vertebrate genomes with Mouse.

Multiple alignments of 4 vertebrate genomes with Mouse Conservation scores for alignments of 4 vertebrate genomes with Mouse. Multiple alignments of 8 vertebrate genomes with Opossum Conservation scores for alignments of 8 vertebrate genomes with Opossum. Multiple alignments of 6 vertebrate genomes with Opossum Conservation scores for alignments of 6 vertebrate genomes with Opossum.

Multiple alignments of 7 vertebrate genomes with Orangutan Conservation scores for alignments of 7 vertebrate genomes with Orangutan. Multiple alignments of 5 vertebrate genomes with Platypus Conservation scores for alignments of 5 vertebrate genomes with Platypus.

Multiple alignments of 19 vertebrate genomes with Rat Conservation scores for alignments of 19 vertebrate genomes with Rat Basewise conservation scores phyloP of 19 vertebrate genomes with Rat FASTA alignments of 19 vertebrate genomes with Rat. Multiple alignments of 12 vertebrate genomes with Rat Conservation scores for alignments of 12 vertebrate genomes with Rat Basewise conservation scores phyloP of 12 vertebrate genomes with Rat. Multiple alignments of 8 vertebrate genomes with Rat Conservation scores for alignments of 8 vertebrate genomes with Rat.

Multiple alignments of 8 vertebrate genomes with Stickleback Conservation scores for alignments of 8 vertebrate genomes with Stickleback. Multiple alignments of 19 mammalian 16 primate genomes with Tariser Conservation scores for alignments of 19 mammalian 16 primate genomes with Tarsier Basewise conservation scores phyloP of 19 mammalian 16 primate genomes with Tarsier FASTA alignments of 19 mammalian 16 primate genomes with Tarsier for CDS regions.

Multiple alignments of 10 vertebrate genomes with X. Multiple alignments of 8 vertebrate genomes with X. Multiple alignments of 6 vertebrate genomes with X. Multiple alignments of 4 vertebrate genomes with X. Multiple alignments of 7 genomes with Zebrafish Conservation scores for alignments of 7 genomes with Zebrafish Basewise conservation scores phyloP of 7 genomes with Zebrafish.

For example, when downloading files to your present directory. To learn more about rsync's options, type "man rsync" on the command line. However, downloading via your browser will be very slow or may even time out for large files i. The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. The user can look at a whole chromosome to get a feel for gene density, open a specific cytogenetic band to see a positionally mapped disease gene candidate, or zoom in to a particular gene to view its spliced ESTs and possible alternative splicing.

The Genome Browser itself does not draw conclusions; rather, it collates all relevant information in one location, leaving the exploration and interpretation to the user. The Genome Browser supports text and sequence based searches that provide quick, precise access to any region of specific interest.

Secondary links from individual entries within annotation tracks lead to sequence details and supplementary off-site databases. To control information overload, tracks need not be displayed in full.

Tracks can be hidden, collapsed into a condensed or single-line display, or filtered according to the user's criteria. Zooming and scrolling controls help to narrow or broaden the displayed chromosomal range to focus on the exact region of interest. Clicking on an individual item within a track opens a details page containing a summary of properties and links to off-site repositories such as PubMed, GenBank, Entrez, and OMIM.

The page provides item-specific information on position, cytoband, strand, data source, and encoded protein, mRNA, genomic sequence and alignment, as appropriate to the nature of the track. A blue navigation bar at the top of the browser provides links to several other tools and data sources. For instance, under the "View" menu, the "DNA" link enables the user to view the raw genomic DNA sequence for the coordinate range displayed in the browser window.

This DNA can encode track features via elaborate text formatting options. The browser data represents an immense collaborative effort involving thousands of people from the international biomedical research community. Although it creates the majority of the annotation tracks in-house, the annotations are based on publicly available data contributed by many labs and research groups throughout the world.

Several of the Genome Browser annotations are generated in collaboration with outside individuals or are contributed wholly by external research groups. UCSC's other major roles include building genome assemblies, creating the Genome Browser work environment, and serving it online. The majority of the sequence data, annotation tracks, and even software are in the public domain and are available for anyone to download. Read more.

Table Browser - convenient text-based access to the database underlying the Genome Browser. Genome Graphs - a tool that allows you to upload and display genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping.

Gene Sorter - expression, homology, and other information on groups of genes that can be related in many ways. To get started, click the Browser link on the blue sidebar. This will take you to a Gateway page where you can select which genome to display.

Note that there are also official mirror sites in Europe and Asia for users who are geographically closer to those continents than to the western United States. To get oriented in using the Genome Browser, try viewing a gene or region of the genome with which you are already familiar, or use the default position.

To open the Genome Browser window:. Occasionally the Gateway page returns a list of several matches in response to a search, rather than immediately displaying the Genome Browser window. When this occurs, click on the item in which you're interested and the Genome Browser will open to that location.

The search mechanism is not a site-wide search engine. However, some types of queries will return an error, e. If your initial query is unsuccessful, try entering a different related term that may produce the same location. For example, if a query on a gene symbol produces no results, try entering an mRNA accession, gene ID number, or descriptive words associated with the gene. If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which it maps in the genome, the BLAT tool will rapidly locate the position by homology alignment, provided that the region has been sequenced.

This search will find close members of the gene family, as well as assembly duplication artifacts. An entire set of query sequences can be looked up simultaneously when provided in fasta format. A successful BLAT search returns a list of one or more genome locations that match the input sequence.

To view one of the alignments in the Genome Browser, click the browser link for the match. The details link can be used to preview the alignment to determine if it is of sufficient match quality to merit viewing in the Genome Browser.

You can open the Genome Browser window with a custom annotation track displayed by using the Add Custom Tracks feature available from the gateway and annotation tracks pages. For more information on creating and using custom annotation tracks, refer to the Creating custom annotation tracks section.

Once you've entered the annotation information, click the submit button at the top of the Gateway page to open up the Genome Browser with the annotation track displayed.

The Genome Browser also provides a collection of custom annotation tracks contributed by the UCSC Genome Bioinformatics group and the research community. NOTE: If an annotation track does not display correctly when you attempt to upload it, you may need to reset the Genome Browser to its default settings, then reload the track. For information on troubleshooting display problems with custom annotation tracks, refer to the troubleshooting section in the Creating custom annotation tracks section.

The Table Browser , a portal to the underlying open source MariaDB relational database driving the Genome Browser, displays genomic data as columns of text rather than as graphical tracks. For more information on using the Table Browser, see the section Getting started: on the Table Browser. Several external gateways provide direct links into the Genome Browser. Journal articles can also link to the browser and provide custom tracks.

Be sure to use the assembly date appropriate to the provided coordinates when using data from a journal source. To facilitate your return to regions of interest within the Genome Browser, save the coordinate range or bookmark the page of displays that you plan to revisit or wish to share with others. It is usually best to work with the most recent assembly even though a full set of tracks might not yet be ready.

Be aware that the coordinates of a given feature on an unfinished chromosome may change from one assembly to the next as gaps are filled, artifactual duplications are reduced, and strand orientations are corrected. The Genome Browser offers multiple tools that can correctly convert coordinates between different assembly releases.

For more information on conversion tools, see the section Converting data between assemblies. To ensure uninterrupted browser services for your research during UCSC server maintenance and power outages, bookmark a mirror site that replicates the UCSC genome browser. Bear in mind that the Genome Browser cannot outperform the underlying quality of the draft genome. Assembly errors and sequence gaps may still occur well into the sequencing process due to regions that are intrinsically difficult to sequence.

Artifactual duplications arise as unavoidable compromises during a build, causing misleading matches in genome coordinates found by alignment.

The Genome Browser annotation tracks page displays a genome location specified through a Gateway search, a BLAT search, or an uploaded custom annotation track. There are five main features on this page: a set of navigation controls , a chromosome ideogram, the annotations tracks image, display configuration buttons , and a set of track display controls. The first time you open the Genome Browser, it will use the application default values to configure the annotation tracks display.

By manipulating the navigation, configuration and display controls, you can customize the annotation tracks display to suit your needs. For a complete description of the annotation tracks available in all assembly versions supported by the Genome Browser, see the Annotation Track Descriptions section.

The Genome Browser retains user preferences from session to session within the same web browser, although it never monitors or records user activities or submitted data. To restore the default settings, click the "Click here to reset" link on the Genome Browser Gateway page. To return the display to the default set of tracks but retain custom tracks and other configured Genome Browser settings , click the default tracks button on the Genome Browser page. Annotation track descriptions: Each annotation track has an associated description page that contains a discussion of the track, the methods used to create the annotation, the data sources and credits for the track, and in some cases filter and configuration options to fine-tune the information displayed in the track.

To view the description page, click on the mini-button to the left of a displayed track or on the label for the track in the Track Controls section. Annotation track details pages: When an annotation track is displayed in full, pack, or squish mode, each line item within the track has an associated details page that can be displayed by clicking on the item or its label.

The information contained in the details page varies by annotation track, but may include basic position information about the item, related links to outside sites and databases, links to genomic alignments, or links to corresponding mRNA, genomic, and protein sequences. Gene prediction tracks: Coding exons are represented by blocks connected by horizontal lines representing introns.

The 5' and 3' untranslated regions UTRs are displayed as thinner blocks on the leading and trailing ends of the aligning regions. In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription. In situations where no intron is visible e. In dense display mode, the degree of darkness corresponds to the number of features aligning to the region or the degree of quality of the match. In pack or full display mode, the aligning regions are connected by lines representing gaps in the alignment typically spliced-out introns , with arrowheads indicating the orientation of the alignment, pointing right if the query sequence was aligned to the forward strand of the genome and left if aligned to the reverse strand.

Two parallel lines are drawn over double-sided alignment gaps, which skip over unalignable sequence in both target and query. For alignments of ESTs, the arrows may be reversed to show the apparent direction of transcription deduced from splice junction sequences. In situations where no gap lines are visible, the arrowheads are displayed on the block itself. To prevent display problems, the Genome Browser imposes an upper limit on the number of alignments that can be viewed simultaneously within the tracks image.

When this limit is exceeded, the Browser displays the best several hundred alignments in a condensed display mode, then lists the number of undisplayed alignments in the last row of the track. In this situation, try zooming in to display more entries or to return the track to full display mode.

For some PSL tracks, extra coloring to indicate mismatching bases and query-only gaps may be available. Chain tracks 2-species alignment : Chain tracks display boxes joined together by either single or double lines. The boxes represent aligning regions.

Single lines indicate gaps that are largely due to a deletion in the genome of the first species or an insertion in the genome of the second species. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species.

In cases where there are multiple chains over a particular portion of the genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the fuller display modes, the individual feature names indicate the chromosome, strand, and location in thousands of the match for each matching alignment. Net tracks 2-species alignment : Boxes represent ungapped alignments, while lines represent gaps.

Clicking on a box displays detailed information about the chain as a whole, while clicking on a line shows information on the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

Individual items in the display are categorized as one of four types other than gap :. Snake tracks: The snake alignment track or snake track shows the relationship between the chosen Browser genome reference genome and another genome query genome.

A snake is a way of viewing a set of pairwise gapless alignments that may overlap on both the reference and query genomes. Alignments are always represented as being on the positive strand of the reference species, but can be on either strand on the query sequence. In full display mode, a snake track can be decomposed into two drawing elements: segments colored rectangles and adjacencies lines connecting the segments.

Segments represent subsequences of the target genome aligned to the given portion of the reference genome. Adjacencies represent the covalent bonds between the aligned subsequences of the target genome.

Red tick-marks within segments represent substitutions with respect to the reference, shown in windows of the reference of by default up to 50 Kb. Zoomed in to the base level, these substitutions are labeled with the non-reference base. An insertion in the reference relative to the query creates a gap between abutting segment sides that is connected by an adjacency. An insertion in the query relative to the reference is represented by an orange tick-mark that splits a segment at the location the extra bases would be inserted.

Simultaneous independent insertions in both query and reference look like an insertion in the reference relative to the target, except that the corresponding adjacency connecting the two segments is colored orange. More complex structural rearrangements create adjacencies that connect the sides of non-abutting segments in a natural fashion. Pack mode can be used to display a larger number of snake tracks in the limited vertical browser. This mode eliminates the adjacencies from the display and forces the segments onto as few rows as possible, given the constraint of still showing duplications in the query sequence.

Dense mode further eliminates these duplications so that each snake track is compactly represented along just one row. Wiggle tracks: These tracks plot a continuous function along a chromosome. Data is displayed in windows of a set number of base pairs in width. The score for each window displays as "mountain ranges" The display characteristics vary among the tracks in this group.

See the individual track descriptions for more information on interpreting the display. If the peak is taller or shorter than what can be shown in the display, it is clipped and colored magenta. Each annotation track within the window may have up to five display modes: Hide: the track is not displayed at all. To hide all the annotation tracks, click the hide all button. This mode is useful for restricting the display to only those tracks in which you are interested.

For example, someone who is not interested in SNPs or mouse synteny may want to hide these tracks to reduce track clutter and improve speed. There are a few annotation tracks that pertain only to one specific chromosome, e. Sanger22, Rosetta. In these cases, the track and its associated controller will be hidden automatically when the track window is not open to the relevant chromosome. Dense: the track is displayed with all features collapsed into a single line. This mode is useful for reducing the amount of space used by a track when you don't need individual line item details or when you just want to get an overall view of an annotation.

For example, by opening an entire chromosome and setting the RefSeq Genes track to dense, you can get a feel for the known gene density of the chromosome without displaying excessive detail. Full: the track is displayed with each annotation feature on a separate line.

It is recommended that you use this option sparingly, due to the large number of individual track items that may potentially align at the selected position. For example, hundreds of ESTs might align with a specified gene. When the number of lines within a requested track location exceeds , the track automatically defaults to a more tightly-packed display mode.

In this situation, you can restore the track display to full mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed. On tracks that contain only hide, dense, and full modes, you can toggle between full and dense display modes by clicking on the track's center label.

Features are unlabeled, and more than one may be drawn on the same line. This mode is useful for reducing the amount of space used by a track when you want to view a large number of individual features and get an overall view of an annotation.

It is particularly good for displaying tracks in which a large number of features align to a particular section of a chromosome, e. EST tracks. Pack: the track is displayed with each annotation feature shown separately and labeled, but not necessarily displayed on a separate line. This mode is useful for reducing the amount of space used by a track when you want to view the large number of individual features allowed by squish mode, but need the labeling and display size provided by full mode.

When the number of lines within the requested track location exceeds , the track automatically defaults to squish display mode. In this situation, you can restore the track display to pack mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed. To toggle between pack and full display modes, click on the track's center label. The track display controls are grouped into categories that reflect the type of data in the track, e.

To change the display mode for a track, find the track's controller in the Track Controls section at the bottom of the Genome Browser page, select the desired mode from the control's display menu, and then click the refresh button. Optional: download from our secondary download server. The tables below previously found per assembly can now be downloaded from the hgFixed database :. Download the appropriate fasta files from our ftp server and extract sequence data using your own tools or the tools from our source tree.

This is the recommended method when you have very large sequence datasets or will be extracting data frequently. Sequence data for most assemblies is located in the assembly's "chromosomes" subdirectory on the downloads server. You'll find instructions for obtaining our source programs and utilities here. To obtain usage information about most programs, execute it without arguments. Use the Table browser to extract sequence.

This is a convenient way to obtain small amounts of sequence. To construct a DAS query, combine an assembly's base URL with the sequence entry point and type specifiers available for that assembly. The entry point specifies chromosome position, and the type indicates the annotation table requested.

You can view the lists of entry points and types available for an assembly with requests of the form:. The Genome Browser source code and executables are freely available for academic, nonprofit, and personal use see Licensing the Genome Browser or Blat for commercial licensing requirements.

The latest version of the source code may be downloaded here. See Downloading Blat source and documentation for information on Blat downloads. Generally, we'd prefer that you not hit our interactive site with programs, unless they are themselves front ends for interactive sites. We can handle the traffic from all the clicks that biologists are likely to generate, but not from programs. Program-driven use is limited to a maximum of one hit every 15 seconds and no more than 5, hits per day.

If you need to run batch Blat jobs, see Downloading Blat source and documentation for a copy of Blat you can run locally. Microsoft Word or any program that can handle large text files will do. Some of the chromosomes begin with long blocks of N s. You may want to search for an A to get past them. Unless you have a particular need to view or use the raw data files, you might find it more interesting to look at the data using the Genome Browser.

Type the name of a gene in which you're interested into the position box or use the default position , then click the submit button. Now you can color the DNA sequence to display which portions are repeats, known genes, genetic markers, etc. Shouldn't they be in synch? Check that your downloaded tables are from the same assembly version as the one you are viewing in the Genome Browser.

If the assembly dates don't match, the coordinates of the data within the tables may differ. In a very rare instance, you could also be affected by the brief lag time between the update of the live databases underlying the Genome Browser and the time it takes for text dumps of these databases to become available in the downloads directory.

The characters most commonly seen in sequence are A , C , G , T , and N , but there are several other valid characters that are used in clones to indicate ambiguity about the identity of certain bases in the sequence. It's not uncommon to see these "wobble" codes at polymorphic positions in DNA sequences. Acids Res. All ESTs in GenBank on the date of the track data freeze for the given organism are used - none are discarded.

When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site. ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found.

Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism.

The maximum intron length allowed by Blat is , bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously i. Start and stop coordinates of each alignment block are available from the appropriate table within the Table Browser. Note that only EST tracks can be viewed at a time within the browser. If more than tracks exist for the selected region, the display defaults to a denser display mode to prevent the user's web browser from being overloaded.

You can restore the EST track display to a fuller display mode by zooming in on the chromosomal range or by using the EST track filter to restrict the number of tracks displayed.