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. 2021 Sep 28;10:e68479. doi: 10.7554/eLife.68479

Figure 7. Tiled-ClickSeq identifies sub-genomic mRNAs, structural variants and Defective-RNAs in clinical samples of SARS-CoV-2.

Similarly to Figure 5B, unique RNA recombination events are plotted for 36 clinical samples as a scatterplot whereby the upstream ‘donor’ site is plotted on the y-axis and a downstream ‘acceptor’ site is plotted on x-axis using the WA-1 reference coordinates for each sample. The read count for each unique RNA recombination event is indicated by the size of the point, while the number of samples in which this each RNA recombination event is found is indicated by the colour-bar. Insertions/duplication/back-splicing events are found above the x = y axis, while deletions and RNA recombination events yielding sgmRNAs are found below.

Figure 7—source data 1. BED files of RNA recombination events detected by ViReMa in the Tiled-ClickSeq data from each WRCEVA isolate and clinical sample.

Figure 7.

Figure 7—figure supplement 1. Tiled-ClickSeq identifies sub-genomic mRNAs, structural variants of clinical samples of SARS-CoV-2.

Figure 7—figure supplement 1.

A table of the most common RNA recombination events found using Tiled-ClickSeq in this study, analogues to Figure 5A. The recombination junctions are indicated on the left of the table, with their relative frequencies indicated in the table and colour-matched for each sample analyzed. All canonical sgmRNAs are found with their open-reading frame (ORF) indicated, in addition to one non-canonical sgmRNAs (*). Three common structural variants including two deletions in spike protein and a deletion in ORF7a are also shown.