See how the pins are numbered? It looks like you've figured that Pin 1 is red, right?
From the sticky:
Skyone wrote:Controller Data (3 Button Controller)
Pin 1 = Brown = Up
Pin 2 = Red = Down
Pin 3 = Orange = Ground/Left
Pin 4 = Yellow = Ground/Right
Pin 5 = Green = 5v
Pin 6 = Blue = Button A/Button B
Pin 7 = Gray = Select
Pin 8 = Black = Ground
Pin 9 = White = Start/Button C

9 pin D-SUB female connector at the controller

9 pin D-SUB male connector at the Genesis
Research by Skyone
Luckily, Sega made it easy on us because they made the pin numbers of the colored wires the same pins of the connector. As you can see, on the PCB where the colored wires go in, the numbering goes:
1, 2, 5, 7, 3, 4, 8, 9, 6
Refer to the above pin -> color diagram above.
1. Brown
2. Red
5. Green
7. Gray
3. Orange
4. Yellow
8. Black
9. White
6. Blue

Tell me if you do not understand.
-Skyler