ABSTRACT Ground motion input layer depth and Vs are crucial parameters in computing representative surface amplification factor, especially for deep deposits where bedrock depth is unknown. For many soil sites, seismic bedrock depth is unknown and randomly assigning the input motion to any layer may result in bias response. The aim of this study is to understand the effect of input layer velocity or depth on surface response parameters. Further determining the appropriate layer for giving the input ground motion for reliable estimation of response parameters by carrying out detailed site-response analysis. For the analysis, surface and bedrock ground motion recordings from KiK-Net downhole are used. Total stress nonlinear site-response analysis has been carried out by varying the velocity and depth to input the ground motion recorded at the bottom most layer for deep and shallow profiles. Using linear mixed effect models on residuals calculated from recorded and predicted surface spectra, fixed bias and σ are calculated. Layer having Vs ≥ 1500 (150) m/s is suitable for capturing the surface amplification spectra for both deep and shallow deposits.