Custom data tracks generated by users can be added directly via the ‘add custom tracks’ button. Only 12 of the 50 currently available track-configuration buttons are shown. Tracks can be configured with a right-click or alternatively by clicking on their name near the bottom of the page. The final track shows a CD8 + epitope from IEDB. Overall, these viruses align well to this region of SARS-CoV-2 (dots indicate identical amino acids) although one non-synonymous substitution (p.Ser1261Pro) is observed in one virus, Rs9401. ![]() The next track (Bat CoV multiz) shows a multiple alignment of 44 bat coronaviruses aligned to the reference. Bar graphs show the frequency of each allele, and mouseover shows the counts of each allele. Below that, a track shows recurrent SARS-CoV-2 variants that have been observed worldwide, as reported by Nextstrain. Here, the NCBI Genes track shows the annotation of the end of the S protein and the start of orf3a, as well as the amino acid translation of their codons. Annotations are shown for data tracks that have been set to visible. The RNA sequence is shown only when the view is sufficiently zoomed in. The search box allows users to search for particular features or to move to exact genomic coordinates. The position bar shows a highlighted red box illustrating the current portion of the genome being viewed. Navigation controls at the top allow users to move left and right and to zoom. Users can also directly enter a nucleotide sequence or the name of a gene (corresponding to the NCBI/INSDC annotation) to go directly to that region of the genome. Coordinates in the position bar should be entered with the prefix NC_045512v2 (the NCBI RefSeq accession of this genome) followed by the stop and start nucleotide numbers (for example, NC_045512v2:25,341-25,401). ![]() The position bar shows the current region of the genome being viewed via a red box, and the search box allows users to manually enter a specific position to view. Clicking the zoom factor ‘base’ zooms in to show the nucleotide bases in the selected region. Buttons in the navigation controls allow users to move left and right along the genomic sequence and zoom in and out by various factors. Above this image are the navigation controls. This sequence is widely used as a standard reference and, because of its early identification, is used as the root genome in phylogenetic trees produced by Nextstrain 6, COVID-19 Genomics UK (COG-UK) 7 and the China National Center for Bioinformation project 8. This reference sequence is the RNA genome isolated from one of the first cases in Wuhan, China, and is known as ‘Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome’ 5. The genome sequence is shown from left to right, 5′ to 3′, as an image with the label NC_045512v2, which is the National Center for Biotechnology Information (NCBI)/International Nucleotide Sequence Database Collaboration (INSD) accession ID for the reference sequence. The UCSC SARS-CoV-2 browser, like alternative genome browsers 2, 3, 4, displays the reference nucleotide sequence of the viral genome and provides an intuitive way to visualize annotations or data on specific parts of the genome (Fig.
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