Giant-Alpecin’s Warren Barguil slammed into the side of the Welshman after losing control on a right-hand bend, forcing Thomas off the road and into a telegraph pole.
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The race leaders were pushing the pace on the technical descent as they chased Vincenzo Nibali, who attacked over the summit of the climb.
It looked like a serious crash, but Thomas was able to get back on his bike and complete the stage. He lost less than a minute to the group of his teammate and race leader Chris Froome, which also contained Alberto Contador (Tinkoff-Saxo), Nairo Quintana (Movistar) and Alejandro Valverde (Movistar).
Young Frenchman Barguil, who managed to stay upright in the incident, reportedly apologised to Thomas for the incident after the stage, which was won by Ruben Plaza (Lampre-Merida) from a breakaway and saw Peter Sagan (Tinkoff-Saxo) take another second place at this Tour.
The descent from the Col de Manse has featured prominently in Tour de France history, with Contador crashing there in 2013 as he tried to put time in to race leader Froome.