The Stratix® V, Arria® V and Cyclone® V handbooks list the total number of General Purpose I/O (GPIO) available for given device variants. This number does not include the number of Transceiver I/O available.
The Quartus® II design software however includes the Transceiver I/O along with the GPIO, in it's total user I/O count, for each device variant.
These device families are offered in multiple configurations where the general purpose I/O count is the same, but the number of Transceiver I/O differs depending upon the number of Transceivers in that device variant. It is therefore advised to use the Quartus II software to decipher the total number of I/O available in a device, including Transceiver I/O.