Four-dimensional cone beam computed tomography (4DCBCT) facilitates verification of lung tumor motion before each treatment fraction and enables accurate patient setup in lung stereotactic ablative body radiation therapy. This work aims to quantify the real-time motion represented in 4DCBCT, depending on the reconstruction algorithm and the respiratory signal utilized for reconstruction. Eight lung cancer patients were implanted with electromagnetic Calypso beacons in airways close to the tumor, enabling real-time motion measurements. 4DCBCT scans were reconstructed from projections for treatment setup CBCT for 1 to 2 fractions of 8 patients with the Feldkamp-Davis-Kress (FDK) algorithm or the prior image constrained compressed sensing (PICCS) method and internal real-time Calypso beacon trajectories or an external respiratory signal (bellows belt). The real-time beacon centroid ("target") motion was compared with beacon centroid positions segmented in the 4DCBCT reconstructions. We tested the hypotheses that (1) the actual target motion was accurately represented in the reconstructions and (2) the reconstruction/respiratory signal combinations performed similarly in the representation of the real-time motion. On average the target motion was significantly underrepresented and exceeded the 4DCBCT motion for 48%, 25%, and 40% of the time in the left-right (LR), superior-inferior (SI), and anterior-posterior (AP) directions, respectively. The average underrepresentation for the LR, SI, and AP direction was 1.7mm, 4.2mm, and 2.5mm, respectively. No difference could be shown between the reconstruction algorithms or respiratory signals in LR direction (FDK vs PICCS: P=.47, Calypso vs bellows: P=.19), SI direction (FDK vs PICCS: P=.49, Calypso vs bellows: P=.22), and AP direction (FDK vs PICCS: P=.62, Calypso vs bellows: P=.34). The 4DCBCT scans all underrepresented the real-time target motion. The selection of the reconstruction algorithm and respiratory signal for the 4DCBCT reconstruction does not have an impact on the reconstructed motion range.