Fig. 2

Single-cell target deep DNA sequencing of BCSCs and non-BCSCs. a Schematic depiction of single-cell target deep DNA sequencing analysis. Pearson correlations between every two samples were determined by the base weight, i.e., the fraction of a base in all four possible bases, at each position in hotspot regions. Binomial test was used to assess the probability of background count (PBC) in the 3 BCSCs from a binomial distribution with the position error rate (PER) determined by 2 non-BCSCs. A PBC lower than the threshold (0.01 here) denotes that the alternative reads cannot all be generated by sequencing errors, i.e., a true SNV is called. b Extremely high Pearson correlations of the genomic program between every two samples (left and middle). The box plot shows no significant differences between the correlation of inter-group samples and that of intra-group samples (right). The P value was determined by a two-tailed t test. c The distribution of genetic distances of each site between every two samples is in a narrow range (left), showing no difference between the inter-group and intra-group at all hotspot sites (ordered by the genetic distance, right). d Constant trend of case-permutation ratio (CPR) of each group following adjustment of the P value threshold. CPR was defined as the ratio of the number of sites with P values less than a threshold in the case group to permutation group