Sounds like the ball landed to the right and behind second base. The question you have to ask now is, did the second basemen have a play on the ball before the runner touched the batted ball, or after. If the runner touched the ball before the second baseman had a play on it, and I don't care if you think the out could have been made as that has no bearing on this play, then the ball is dead, runner is out, batter is placed on first with other runners being placed back on the bag last touched, and the runners only moving forward if forced.
If the the 2b already had a play on the ball, missed it, regardless if he touched the ball or not, then you have a live ball and runner is free to move forward as the ball has passed a fielder. The only way that the runner could be called out in this scenario is if the umpire determined that the runner did something intentional to touch the ball.
Live and dead ball, along with the out or safe call, is dependent on if the ball has passed a fielder before touching the runner.