Fig. 4: Using the WashU Virus Genome Browser to study sequence conservation across viral species.

Genome-browser view of the 5′ end of the SARS-CoV-2 S gene. Tracks loaded in the view are as follows from top to bottom: gene annotations, ruler, transcription regulatory sequence (TRS) sites, pangolin coronavirus (EPI_ISL_410721) comparison tracks (SNV track, genome-alignment track and read-alignment track) and bat coronavirus (EPI_ISL_402131) comparison tracks (SNV track, genome-alignment track and read-alignment track). In the SNV track (displayed in density mode), the y axis represents the density of sequence variation in bat or pangolin coronaviruses compared with the SARS-CoV-2 reference. In the genome-alignment track, the SARS-CoV-2 reference is represented by the solid blue band, and the query sequence (in this case, the bat or pangolin coronavirus genome) is represented by the purple band. Black bars between the reference and the query represent matches, whereas the absence of a bar represents a variant (mismatch or gap). A gap in the reference or query is represented by a gap in the blue or purple band, respectively. In the read-alignment track, data are loaded in bam format. Each read is displayed as a colored bar (blue, plus strand; red, minus strand), and gaps within a bar represent mismatches to the reference. The alignment of a read to the reference can be displayed by selecting a particular read (pop-up display window). This genome-browser view shows that the 5′ end of the S gene is highly variable between SARS-CoV-2 and the pangolin coronavirus, but not between SARS-CoV-2 and the bat coronavirus.