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. +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 | @@ -71,41 +71,41 @@
|---|---|
| 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:
@@ -140,62 +140,62 @@
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. +the perspective of the genomic sequence. Also, in bosTau9, galGal5, rheMac10, +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.
+ +EVA Release 7 MakeDoc.Note: It is not recommended 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.
+of interest, e.g. evaSnp7.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/$db/bbi/evaSnp6.bb -chrom=chr21 -start=0 -end=100000000 stdout
+bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/evaSnp7.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.