braking, all ok until I nearly depress all the way then it starts making a noise on 2004 Volkswagen Jetta

OK, I have called my mechanic but he hasn't called me back yet and am concerned...
When I depress the brake pedal everything is ok until I get to the "bottom" of the pedal, you know, keep pushing down, then poof, it starts making wonky noises. It is a low grumbly noise. Almost grinding but not quite. The noise is coming from the back of the car and almost sounds like the trunk.
To make do, I am downshifting and using the brakes as little as possible.
Any thoughts?
Thank you,

Asked by for the 2004 Volkswagen Jetta
start to check all brake lines for leak and check master cylinder.