Analysis of large deletions in iPSC single-cell clones. a Raw deletion indexes of iPSC single-cell clones. Clone #31 highlighted in red indicated the only one clone with significant deletion mutation on one allele among 52 gene-edited iPSC single-cell clones. See details of all the clones in Additional file 1: Fig. S10. b Heterozygous genotype of the two SNPs identified on the BCL11A alleles. c No loss of heterozygosity in all the iPSC single-cell clones by SNP analysis. A total of 52 edited single-cell clones were analyzed by PCR and nanopore sequencing. d Assessment of mega-deletions in edited iPSC single-cell clones by qPCR analysis. We conducted qPCR to assess copies of gDNA at 40, 80, and 160 kb away from the target site BCL11A-1. AAVS1, located on another chromosome, served as a control. The data from WT cells were used to normalize the copy numbers of edited cells. We aggregated all the data points surrounding the BCL11A-1 editing site of each clone to increase statistical power. The data in c and d were statistically analyzed by a two-way ANOVA test. “ns” means no significance (P > 0.05).