You can't calculate an average across all industries. That does not make any sense to do. As an example, men choose to work more dangerous jobs than women in industries that tend to pay higher (miners, oil rigs, etc).
If you want to play fair, as this paper did, and consider a particular job type (highly paid executives), it would make sense to start calculating averages or percentages.
I don't think this washington post article really proves anything about the discrimination women experience within the workplace, after getting hired. We do know that the gender balance is unequal in the STEM workforce, and for various reasons, some employers feel compelled to try to balance that ratio by hiring more women. However, this does not mean women experience greater upward mobility after entering the organization.
You just dismissed real evidence that men are discriminated against as being completely justified, and then implied that discrimination against women exists once in the workplace without a shred of evidence.
Companies are clearly working hard to discriminate against men when hiring, and without evidence the default conclusion should be that they do the same thing within organizations when handling promotions.
95 out of every 100 workplace deaths are men.
If you are looking for a reason women are paid less, look at this. The lowest paying majors are completely dominated by women: http://www.npr.org/sections/money/2013/09/11/220748057/why-w...
In fact, equally qualified women are twice as likely to be hired as men: https://www.washingtonpost.com/news/morning-mix/wp/2015/04/1...