The JTAG mode is also a serial configuration mode, popular for prototyping and highly used for board test. The four-pin JTAG boundary-scan interface is common on board testers and debugging hardware. The AMD programming cables for FPGAs use the JTAG interface for prototype download and debugging. Regardless of the primary configuration mode used in a application, the physical JTAG configuration mode pin setting should be included to ease design development and debug. See the following figure for details.
Figure 1. JTAG Configuration Mode