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Transformation domain interference suppressions (TD-IS) are effectively used to enhance the global navigation satellite system (GNSS) receiver, but simultaneously they intrinsically affect on Pseudo-Noise (PN) code tracking loops, which offer the precise chip synchronization to GNSS receiver. In this paper, we provide a simple general model for different TD-IS methods and analytical expressions for TD-IS effects on PN code tracking loops. The model includes common property of different TD-IS methods, such as DFT-based frequency excision (DFT-FE) and filter-bank-based interference suppression (FB-IS). Traditionally, the GNSS receiver operates Binary Phase Shift Keying (BPSK) modulation with direct sequence spread spectrum (DSSS) signal or Binary Offset Carrier (BOC) modulation with DSSS signal. Tracking loops adopted include coherent early-late PN code tracking loop (CELL) and non-coherent early-late PN code tracking loop (NELL). By using the general model, analytical expressions derived give the positioning precision error (PPE) performance about TD-IS methods acting on CELL and NELL with BPSK-DSSS or BOC-DSSS signal in the GNSS receiver. Finally, numerical results confirm the TD-IS not cause the precision bias and when interferences exist in the GNSS signal, the CELL with the BOC-DSSS signal takes on better PPE performance under the TD-IS processing.