We report on a first principles analysis of quantum transport through molecular wires made of 4,4'bipyridine and 6-alkanedithiol contacted by Au electrodes. We investigate how charge transport is altered due to small structure changes at the molecule-electrode contacts. These changes include distance between the molecule and the contact, extra metal atoms at the Au surface, binding sites, molecular orientation, and bias voltages. By investigating hundreds of wires we extract a statistical picture on transport properties of the two different molecules. We compare quantitatively with the corresponding experimental data.