The transcriptional and translational landscape of equine torovirus

Hazel Stewart; Katherine Brown; Adam M. Dinan; Nerea Irigoyen; Eric J. Snijder; Andrew E. Firth

are utilised for N protein gene sgRNA synthesis. RNA sequencing reads that did not 216 map to either the viral genome or host databases were analysed for containing 217 potential viral chimaeric junctions, indicative of leader-to-body joining during 218 discontinuous sgRNA synthesis ( Figure 4 ). Relative abundances were calculated by 219 normalising read counts to the number of non-chimaeric reads spanning each 220 junction. Between the two replicates combined, 8330 reads were identified as 221 chimaeras, mapping to 2837 putative junction sites. Of these, 213 were considered 222 to be highly supported by the data, either due to being identified in at least 10 223 chimaeric reads or containing the full 5' leader and TRS sequence. Adjacent donor or 224 acceptor sites were then merged (see Materials and Methods), leaving 70 unique 225 junctions ( Figure 4) . 226