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Programming UV EPROMs
This is the most straightforward way to program UV EPROMs, and is my preferred way to program 27C160 and 27C322 chips for the Advanced UV boards.
The GQ4x4 includes a programming adapter board with ZIF sockets. Before programming a 27C160 or 27C322, you have to configure J1 to the proper setting (boxed in red). Move the jumper to the top two pins to program 27C160s, or to the bottom two pins to program 27C322s.

Make sure when you place the adapter board in the ZIF socket that you line up the 36 (2x rows of 18) header pins on the bottom of the socket. There should be four empty pins on the top.

Open the GQ4x4 software, and select the proper IC from the Device list on the left bar, or in the top menu. (You can pull this up with CTRL+D)

Click the "Blank Check" button to make sure your chip is blank. Note that if your chip is dead, or you have poor connections, you may read a blank when the chip actually is not blank.
Load the ROM file using the top menu, and when prompted, select the Binary file format.

You can see the ROM data in the "Buffer" tab.

Before you program the file, you need to make sure it has proper endianness. If it does not, you need to do a byteswap. An easy way to tell this is by looking at the ASCII data at the top of the ROM - if it says "ESAGG NESESI" instead of "SEGA GENESIS" (or "ESAGM GE ARDVI E" instead of "SEGA MEGA DRIVE") then you've got it correct. If not, then you will need to byte swap your ROM. To do this, just click the "A<>B" button at the top.

Now click the "Write" button to write the data to the ROM. If programming fails immediately, then you either have a bad chip or a poor connection, or a wrong configuration. If it fails in the middle of programming, then you may have a faulty chip.
See the tutorial in the 27C322-TL866 Adapter repository. Remember that this adapter still works with the T48 programmer.