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Braga took the lead early through midfielder Florian Grillitsch in the 5th minute, marking his second consecutive goal in the competition following his strike against Ferencváros in the Round of 16.
A goal by Betis defender Marc Bartra was ruled out for offside by VAR in the 7th minute.
Colombian forward Cucho Hernandez converted a penalty in the 61st minute to equalize for the Spanish side.
The decisive second leg will take place next Thursday in Spain.