The ML trees and ancestral states reconstructed by CNETML for patient 20. 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. For patient 20, the samples taken at 12 months before final endoscopy location 2 (20_12_2) is Indeterminate (ID), the final endoscopy at location 2 (20_0_2) is Low-Grade Dysplasia (LGD), and all the other samples are Non-dysplastic BE (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
