To test the reproducibility of the PASSPORT-seq bioassay, we first performed the assay with five biological replicates in each of the three cell lines and compared the number of reads from two of the five biological replicates. The input plasmid libraries had representation of all 100 allelic pairs. The R2 value for the comparison of sets of two of the five input normalized-biological replicates within the same sequencing run was between 0.68 and 0.98 (p < 0.05; Supplementary Figure 4) demonstrating highly reproducible results within a run.
