Extended Data Fig. 4: SPRINTER’s replication-aware framework enables the differentiation of RDR fluctuations due to either replication or CNAs.

a, Average RDRs (y axis) were measured by SPRINTER in 50 kb genomic bins with either early (magenta) or late (green) replication timing across autosomes in the genome (x axis) for 73 mid-S-phase cells in the generated tetraploid ground truth dataset assigned to the same clone by SPRINTER. b, A replication timing profile (RTP, y axis) is calculated by SPRINTER for each bin (x axis) for the same cells by correcting RDRs for CNAs based on the copy-number segments inferred by SPRINTER, preserving clear fluctuations between bins with different replication timing (with magenta early regions having higher RDRs than green late regions on average). c, Replication-corrected RDRs (y axis) are computed by SPRINTER for each bin (x axis) for the same cells by correcting RDRs for replication fluctuations, such that the remaining fluctuations are likely due to CNAs and are not influenced by replication (in each segment there is no clear difference between bins with different replication timing).