sgDI-tector detects most canonical sgRNAs in all replicates with a high number of counts. (Left panels) Deletion DVGs distribution across the last 10 kb positions of the SARS-CoV-2 genome (GISAID ID: EPI_ISL_414631). Each blue or orange bar corresponds to a deletion, the position of the bar being the starting point of the “body” part of the junction (called RI position in sgDI-tector). Crosses are expected RI positions from Alexandersen et al. (2020), and bars are colored in orange if the deletion is observed in that position in our data. (Right panels) Number of counts and ORF name for the 13 deletions with most counts observed in each replicate. Orange bars correspond to orange crosses in the left panel and represent canonical TRS. Blue bars correspond to putative noncanonical ORFs detected in our data. Names for noncanonical ORFs are hexadecimal numbers representing the position of the corresponding start codon (AUG) in the standard 5′-to-3′ sense in the reference sequence (GISAID ID: EPI_ISL_414631), see also Supplemental Table 2.
