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Head coach Ady Pennock hailed the goal that finally broke Gills’ resolve on Tuesday night.
A super strike from Republic of Ireland under-21 international Liam Kelly put Reading 1-0 up in the Carabao Cup game and the Championship side were untroubled after that.
Pennock said: “It was a worldy to break the deadlock.
“Goals change games and just before they scored we had a chance through Tom Eaves. You just never know do you, what could have happened.
“You have to give their goalkeeper credit, it was a great save (from Eaves), the whole stadium was standing up clapping it.
“Reading showed their quality, which they have got, to then put the ball in the top corner (at the other end).”
Match Report: Reading 2 Gillingham 0
It was a great test for the Gills, up against a side who like to pass the ball around.
Pennock said: “We had a good go and we are playing against a team who are very good, like the Arsenal of the Championship.
“I hope no other teams (in League 1) play like that but you have to give Reading credit.
“I want to wish them all the best in the next round because they are a very good side, it was a great stadium to visit and I think the young boys got a lot out of it.
“First half we had two or three half chances and just before they scored we had a great chance through Eaves and their keeper did a really good save. Those moments change games.
“There were some good positives to take and we were up against a good side. We created some good chances and maybe there are some Championship clubs who will come here and not create as many chances as we did.
“We don’t want to lose, obviously, nobody was down there (in the changing rooms afterwards) telling jokes. We lost the game 2-0, nobody has gone in there with a clown suit on.
“We gave a good account of ourselves. The confidence is there. Everyone is pulling together in the right direction, there is a lot of desire now and it is a good changing room.”