Fig. 3

Bias and chimeras comparison using WGS data. a The cumulative distribution of sequencing fold depth of deep WGS data amplified by DOP-1, MDA-2, MDA-3, and MALBAC, respectively. The standard Poisson Cumulative Distribution (λ = 30) is plotted (dashed), and YH-mix and SW480 bulk data are presented as a control. It was related to Additional file 11: Table S6. b Normalized read depth distribution in repeat regions (Alu and L1 regions) and the entire genome of deep-sequenced data amplified by different WGA kits. The normalized read depth is calculated for each Alu/L1 region and for each window binning 100 kb of the entire genome. c Normalized read depth distribution in regions with different GC content of deep-sequenced data amplified by different WGA kits. The 100 kb windows with GC content >50 % are defined as ‘HighGC’ windows, <35 % as ‘LowGC’ windows, and others as ‘MiddleGC’ windows. d Histogram of effective consensus genotype efficiency, and line graph of the concordant ratio of all deep-sequenced cells amplified by different WGA kits compared to the golden control. e The percentage of different types of chimeras detected in MDA-2-amplified YH single cells. CTX, inter-chromosomal translocation; ITX, intra-chromosomal translocation; DEL, deletion: INS, insertion: INV, inversion. f Boxplot of the length distribution of ITXs shared between MDA-2-amplified cells and YH-mix versus the chimera ITXs that are unique in single cells. p < 0.01, Mann–Whitney-Wilcoxon test