Figure 2.

SARS-CoV-2 produces classes of TRS-independent sgRNA, which are abundantly expressed

The transcript nomenclature W_X,Y_Z indicates that the transcript consists of the continuous segment from W to X joined with the segment from Y to Z.

(A) Total depth of coverage summed over all cDNA sequencing runs by categorization of reads based on mapping to 5′ and 3′ end of virus (within 10 base pairs [bp]) plotted on a log y scale. Dashed lines indicate location of TRS motifs, with alternative motifs detected using FIMO shown in dotted and dot-dash lines.

(B) Transcript abundance of major classes of sgRNA in TPMs mapped viral reads, plotted on a log scale for dRNA experiments (bottom row) and direct cDNA (top line). 95% CIs estimated from binomial model using the logistic parameterization.

(C) Transcript coverage of major classes of sgRNA in terms of total read depth across all cDNA samples, shown on log scale. Dashed lines indicate positions of TRS motif.

(D) Coverage of TRS-dependent sgRNA (blue) versus TRS-independent RNA (orange), summed over all cDNA sequencing experiments. Black dashed lines indicate position of TRS motifs. y axis is on log scale.

(E) Enlarged schematic of genome annotation for SARS-CoV-2. Regions are to scale.

See also Figure S1.