"Wearing the yellow jersey is a massive honour". He has won back-to-back stages in the Alps.
The question now for Team Sky is whether four-time defending champion Froome remains the team leader, or whether that honor switches to form man Thomas.
And for a long while, it looked like Thomas's lead was in danger when Dutchman Steven Kruijswijk launched an audacious attack after he had squeezed into an early breakaway. "I could lose 10 minutes".
Van Avermaet, who is not a specialist climber, appeared under threat at the beginning of the 158.5 km race from Annecy featuring four categorised climbs and with a downhill finish into Le Grand Bornand. Since then, however, he has confirmed his credentials with two brilliant rides high up in the mountains. Froomey knows how to win a three-week race.
The Welshman survived a brutal final few kilometers on the switchbacks and then turned on the afterburners in the last few hundred meters to win the day.
"I did say yesterday this race is made for me, after today that's it, I can be happy for sure now".
"It is very emotional, I went through such a hard period so today is pure happiness", said Degenkolb, who suffered several fractures and a serious finger injury after he and some team mates were hit by a vehicle during a training ride in January 2016.
The next truly decisive day could come on Stage 17, an outlier at just 40 miles long with a summit finish on the Col du Portet.
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There was talk before and during this year's Tour that Thomas could challenge Froome as Sky's team leader, even though Froome has won the last three Grand Tours.
"Dumoulin, who finished runner-up to Froome in May's Giro d'Italia, is third on GC at 1'50" with Nibali and Roglic impressively limiting their losses to stay in the top five, at 2'37" and 2'46" respectively. And he is showing no signs of slowing down.
A day after the first rest day, the big guns were in no mood to take risks ahead of two more stages in the Alps.
Kittel and Renshaw both finished just under 45 minutes behind stage victor Geraint Thomas of Team Sky but still failed to make the cut.
"It's an fantastic position for us", Froome said. "It's still a nice position to be in", he said. But he was caught by Froome on the way up to Huez with 3.5 kilometres remaining. He seemed to back that up, if only briefly, on the road Thursday. From there, he mostly followed wheels. "When Froome attacked I went after him and felt good".
Thomas will wear the yellow jersey when the Tour continues from Bourg-Saint-Maurice Les Arcs around 21 bends to the notorious Alpe d'Huez. It remains to be seen whether he can keep this up into the Pyrenees.
Fueled by previous disappointments and thoughts of his ill father watching on TV, Alaphilippe timed his break perfectly and powered to victory on the first day in the mountains, crossing the line alone, and finishing well ahead of his rivals for his first Tour win.