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