The ML trees and ancestral states reconstructed by CNETML for patient 51. The bootstrap support values are shown in coloured rectangles with lighter colours suggesting stronger support. The coloured bars at the internal nodes show the confidence intervals of node ages. Each sample is denoted by patientID_timeID_locationID, where timeID is the month before final endoscopy and locationID is the relative esophageal sample location. There are two sets of samples taken at the same time and location for patient 51, which are indicated by _2 at the end. For patient 51, the samples taken at 36 months before final endoscopy location 2 and 3 (51_36_2 and 51_36_3) are IDs, the sample taken at 60 months before final endoscopy at location 2 (51_60_2) is LGD, and all the other samples are NDBE. The cancer-related genes overlapping with the reconstructed CNPs are shown on the branches (red: copy number gain, blue: copy number loss). The confidence intervals of duplication/deletion rates are shown in parentheses in the title of the plot for each patient
