Fig. 3

Non-canonical junctions accumulate over time in cell culture. a Illustration of computational approach used to determine change in junction percentages over time. For each position in the SARS-CoV-2 genome and separately for 5′ and 3′ junctions, the number of junctions at that position was calculated. Using these numbers, the percentage of 5′ or 3′ junctions falling at each position was calculated. The change in junction percentage at each position is defined as the difference between the position’s junction percentage at the late and early timepoints, and this junction change was plotted for each position. b–e The change in junction percentage for 5′ (orange) and 3′ (blue) junctions over time in the Finkel (b, d) and Emanuel (c, e) datasets was determined as described above. Changes in the percentage of junctions Positions with at change greater than 2.5% are annotated with text on the plot. Panels d and e are zoomed in versions of b and c. f, g Junctions were assigned into groups based on their 5′ and 3′ junction positions. If a junction had a 5′ end within 20 bases of the TRS-L and within 15 bases of a TRS-B, it was considered a canonical junction belonging to the ORF with a start closest to the TRS-B. Otherwise, it was considered non-canonical. The percentage of junctions falling into each category was calculated for early and late timepoints, and the difference between each category’s percentage in the late vs early timepoint was plotted