Fig. 1

Characterization of RD signal in cancer genome. a The RD frequency distribution (left) and genome-wide coverage plot of all chromosomes (right) of A427 cell line showing the presence of widespread LCVs. b Coverage plot of chromosome (Chr) 2 showing LCVs of different CN states. c Zoomed in view of Chr 2 (184–215 Mb) shows the presence of FAs (both amplifications and deletions) inside the LCV. The blue curved lines in (b) and (c) denote the upper envelope of RD signal showing the regions affected by wave artifacts. Few loci of focal amplifications and deletions are indicated. d RD frequency distributions of a normal genome (HG00119) and different cancer cell lines showing the estimation of the CN reference (2N) by CNAtra (solid blue line). The black line denotes the global RD median, while the dotted blue lines indicate the higher CN states (3N, 4N, 5N) based on CNAtra CN reference