Figure 3.

Structure map of the full SARS-CoV-2 genome in vitro. Map of the SARS-CoV-2 genome depicting (top to bottom): median SHAPE reactivity (in 50 nt centered windows, with respect to the median reactivity across the whole genome), median DMS reactivity (in 50 nt centered widows, with respect to the median reactivity across the whole genome), Shannon entropy and base-pairing probabilities for both the SHAPE (up) and DMS (down) samples, set of low SHAPE – low Shannon helices coherently predicted in both datasets. Regions with both low Shannon and low SHAPE, likely identifying RNA segments with well-defined foldings, are marked in grey. Two regions of low sequencing coverage are marked in red.