< evaSnpContainer | These tracks contain mappings of single nucleotide variants < evaSnpContainer | and small insertions and deletions (indels) < evaSnpContainer | from the European Variation Archive < evaSnpContainer | (EVA) < evaSnpContainer | for the cow bosTau9 genome. The dbSNP database at NCBI no longer < evaSnpContainer | hosts non-human variants. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Variants are shown as single tick marks at most zoom levels. < evaSnpContainer | When viewing the track at or near base-level resolution, the displayed < evaSnpContainer | width of the SNP variant corresponds to the width of the variant in the < evaSnpContainer | reference sequence. Insertions are indicated by a single tick mark displayed < evaSnpContainer | between two nucleotides, single nucleotide polymorphisms are displayed as the < evaSnpContainer | width of a single base, and multiple nucleotide variants are represented by a < evaSnpContainer | block that spans two or more bases. The display is set to automatically collapse to < evaSnpContainer | dense visibility when there are more than 100k variants in the window. < evaSnpContainer | When the window size is more than 250k bp, the display is switched to density graph mode. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Navigation to an individual variant can be accomplished by typing or copying < evaSnpContainer | the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the < evaSnpContainer | Browser.
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | A click on an item in the graphical display displays a page with data about < evaSnpContainer | that variant. Data fields include the Reference and Alternate Alleles, the < evaSnpContainer | class of the variant as reported by EVA, the source of the data, the amino acid < evaSnpContainer | change, if any, and the functional class as determined by UCSC's Variant Annotation < evaSnpContainer | Integrator. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |Variants can be filtered using the track controls to show subsets of the < evaSnpContainer | data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or < evaSnpContainer | by color, which bins the UCSC functional effects into general classes.
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Mousing over an item shows the ucscClass, which is the consequence according to the < evaSnpContainer | Variant Annotation Integrator, and < evaSnpContainer | the aaChange when one is available, which is the change in amino acid in HGVS.p < evaSnpContainer | terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over < evaSnpContainer | in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID < evaSnpContainer | separated by spaces describing all possible AA changes.
< evaSnpContainer |< evaSnpContainer | Multiple items may appear due to different variant predictions on multiple gene transcripts. < evaSnpContainer | For all organisms, the gene models used were the NCBI RefSeq curated when available, if not then < evaSnpContainer | ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Variants are colored according to the most potentially deleterious functional effect prediction < evaSnpContainer | according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section < evaSnpContainer | below. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer |
| Color | < evaSnpContainer |Variant Type | < evaSnpContainer |
|---|---|
| Protein-altering variants and splice site variants | |
| Synonymous codon variants | |
| Non-coding transcript or Untranslated Region (UTR) variants | |
| Intergenic and intronic variants |
< evaSnpContainer | Variants are classified by EVA into one of the following sequence ontology terms: < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Data were downloaded from the European Variation Archive EVA < evaSnpContainer | current_ids.vcf.gz files corresponding to the proper assembly.
< evaSnpContainer |< evaSnpContainer | Chromosome names were converted to UCSC-style < evaSnpContainer | and the variants passed through the < evaSnpContainer | Variant Annotation Integrator to < evaSnpContainer | predict consequence. For every organism the NCBI RefSeq curated models were used when available, < evaSnpContainer | followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models < evaSnpContainer | were possible.
< evaSnpContainer |< evaSnpContainer | Variants were then colored according to their predicted consequence in the following fashion: < evaSnpContainer |
< evaSnpContainer | Sequence Ontology ("SO:") < evaSnpContainer | terms were converted to the variant classes, then the files were converted to BED, < evaSnpContainer | and then bigBed format. < evaSnpContainer |
< evaSnpContainer |< evaSnpContainer | No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). < evaSnpContainer | These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). < evaSnpContainer | Amino-acid substitutions for missense variants are based < evaSnpContainer | on RefSeq alignments of mRNA transcripts, which do not always match the amino acids < evaSnpContainer | predicted from translating the genomic sequence. Therefore, in some instances, the < evaSnpContainer | variant and the genomic nucleotide and associated amino acid may be reversed. < evaSnpContainer | E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from < evaSnpContainer | the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, < evaSnpContainer | danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. < evaSnpContainer | For complete documentation of the processing of these tracks, see the makedoc corresponding < evaSnpContainer | to the version of interest. For example, the < evaSnpContainer | < evaSnpContainer | EVA Release 6 MakeDoc.
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Note: It is not recommended to use LiftOver to convert SNPs between assemblies, < evaSnpContainer | and more information about how to convert SNPs between assemblies can be found on the following < evaSnpContainer | FAQ entry.
< evaSnpContainer |< evaSnpContainer | The data can be explored interactively with the Table Browser, < evaSnpContainer | or the Data Integrator. For automated analysis, the data may be < evaSnpContainer | queried from our REST API. Please refer to our < evaSnpContainer | mailing list archives < evaSnpContainer | for questions, or our Data Access FAQ for more < evaSnpContainer | information.
< evaSnpContainer | < evaSnpContainer |
< evaSnpContainer | For automated download and analysis, this annotation is stored in a bigBed file that
< evaSnpContainer | can be downloaded from our download server. Use the corresponding version number for the track
< evaSnpContainer | of interest, e.g. evaSnp6.bb.
< evaSnpContainer | Individual regions or the whole genome annotation can be obtained using our tool
< evaSnpContainer | bigBedToBed which can be compiled from the source code or downloaded as a precompiled
< evaSnpContainer | binary for your system. Instructions for downloading source code and binaries can be found
< evaSnpContainer | here.
< evaSnpContainer | The tool can also be used to obtain only features within a given range, e.g.
< evaSnpContainer |
< evaSnpContainer | bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/bosTau9/bbi/evaSnp6.bb -chrom=chr21 -start=0 -end=100000000 stdout
< evaSnpContainer |
< evaSnpContainer | This track was produced from the European < evaSnpContainer | Variation Archive release data. Consequences were predicted using UCSC's Variant Annotation < evaSnpContainer | Integrator and NCBI's RefSeq as well as ensembl gene models. < evaSnpContainer |
< evaSnpContainer | < evaSnpContainer |< evaSnpContainer | Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, < evaSnpContainer | Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all < evaSnpContainer | species. Nucleic Acids Res. 2021 Oct 28:gkab960. < evaSnpContainer | doi:10.1093/nar/gkab960. < evaSnpContainer | Epub ahead of print. PMID: 34718739. PMID: PMC8728205. < evaSnpContainer |
< evaSnpContainer |< evaSnpContainer | Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, < evaSnpContainer | Haussler D, Kent WJ. < evaSnpContainer | UCSC Data Integrator and Variant Annotation Integrator. < evaSnpContainer | Bioinformatics. 2016 May 1;32(9):1430-2. < evaSnpContainer | PMID: 26740527; PMC: < evaSnpContainer | PMC4848401 < evaSnpContainer |
< evaSnpContainer | 4687,4699d4469 < rmsk |< rmsk | When analyzing the data tables of this track, keep in mind that Repbase is not the same < rmsk | as the Repeatmasker sequence database and that the repeat names in the < rmsk | Repeatmasker output are not the same as the sequence names in the Repeatmasker < rmsk | database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker < rmsk | output and this track, but there is not necessarily a single sequence "L1PA4" < rmsk | in the Repeatmasker database. This is because Repeatmasker creates annotations < rmsk | by joining matches to partial pieces of the database together so there is no < rmsk | 1:1 relationship between its sequence database and the annotations. To learn < rmsk | more, you can read the Repeatmasker paper, its source code or reach out to the < rmsk | Repeatmasker authors, your local expert on transposable elements or us. < rmsk |
< rmsk | 5788,5793c5558,5561 < uniprot | Features in the "UniProt Modifications" (modified residues) track are drawn in < uniprot | light green. Disulfide bonds are shown in < uniprot | dark grey. Topological domains < uniprot | in maroon and zinc finger regions in < uniprot | olive green. < uniprot | --- > uniprot | In the "UniProt Modifications" track, lipoification sites are highlighted in > uniprot | dark blue, glycosylation sites in > uniprot | dark green, and phosphorylation in > uniprot | light green.