(a) Simulations of alternative splicing and scRNA-seq under the binary-bimodal model, in which each cell produces one isoform or the other, but rarely both. As in Figure 2b, each row of the histogram shows for one intermediate exon across all cells. The observed distribution is similar to the true distribution, and its shape is largely unaffected by capture efficiency. (b) Simulations with the non-binary, unimodal model, in which most cells present a mixture of the two alternative isoforms. Exons with high expression have a unimodal distribution of true . Low capture efficiency results in an increase in binary observations (only one isoform observed), leading to a distortion of the observed distribution of to look bimodal. Only a handful of the highest expressed exons maintain a unimodal distribution of . Fewer exons show unimodal splicing as the capture efficiency is reduced. (c) Under the binary-bimodal model, exons with high coverage have slightly fewer binary observations, and (d) simulated cells with a high number of total splice junction reads have slightly fewer exons with binary . (e) Under the unimodal model, exons with intermediate splicing show a strong decrease in binary observations as coverage increases, as seen in real data (Figure 2c). (f) Similarly, simulated cells with high read coverage have a decrease of the proportion of binary . (g) Effect of capture efficiency on the proportion of binary observations of cassette exons with underlying = 0.5. (h) Effect of the initial number of mRNA molecules and underlying on the proportion of binary observations.