Copy Number profiles for sample TSB000156, with the CN agreement plot. Prior to plotting, numeric CN is translated to CN Call; “High Loss”, “Loss”, “ND”, “Gain” and “High Gain” with numeric CN conditions; “CN < 1”, ”1 ≤ CN < 2”, “CN = 2”, “3 ≥ CN > 2” and “CN > 3” respectively. Events smaller than 1 Megabase are plotted as dashed lines. Red represents CN gains (dark red is “High Gain”), green represents loss (dark green is “High loss”). Panels A), B) and C) show the replicate CN profiles of sample TSB000156 run at three independent laboratories. Regions of LOH are plotted along the CN State = ND line as yellow bars. Panel D) shows the percentage of sites that agree on a given CN event along the length of the whole genome. GW-CN-Call-Agreement describes the percentage of the length of the genome for which all three independent laboratories agreed on the CN Call, in this case 94.7%. Similarly for LOH the percentage of the length of the genome for which all three independent laboratories agreed on LOH status is 99.1%. Noteworthy in this example is the out of bounds ndSNPQC value (<26) producing remarkably reproducible CN data.