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I am assuming that your '99 is a 6 speed. The 3.42 rear gear ratio was standard for the 6 speed. I don't think you had any other option with the manual transmission. The automatic had a std 2.73 and I think could be upgraded to a 3.15(?).
All 6spd cars were 3.42, no optional ratios.
Automatic cars came standard with 2.73. 3.15 was optional.
Simply put, the higher the numerical ratio, the faster the car will accelerate, and it will be running at a higher rpm in any given gear at the same speed.
Aftermarket ratios offered are 3.73, 3.90, and 4.10 for those wishing even more. The 3.42 ratio is also a popular upgrade for A4 owners.