18.104.22.168. Programming Serial Flash Devices using the AS Interface
You must set MSEL to JTAG. When MSEL is set to JTAG, the SDM tristates the following AS pins: AS_CLK, AS_nRST, AS_DATA0-AS_DATA3, and AS_nCSO0-AS_nCSO3. The Intel® Quartus® Prime Programmer programs the flash memory devices via the AS header. If you are using the Generic Serial Flash Interface Intel® FPGA IP to write the flash memory the flash device must be connected to GPIO to access the flash device.