England were awarded five penalty runs on day two of the second Test against Sri Lanka because the umpires deemed Roshen Silva to be deliberately short of his crease. That meant that England's first innings tally went from 285 to 290.
The incident happened in the first ball of the 86th over. Jack Leach was the bowler and Roshen Silva cut the ball towards the third man boundary where Moeen Ali ensured that it didn't go for a boundary and the batsmen ran two. However, in the process, Silva failed to ground his bat while running the first run and completed the second run.
The two umpires converged and deemed that it was a deliberate short run as the batsman had ample title to ground his bat and complete the first run before going for a second, even if he thought that the ball was going for a boundary.
First, a dead ball was signalled then, the umpire awarded five penalty runs to England. No runs were awarded off the ball, which itself was deemed a legal delivery.
Law 18, which deals with scoring runs and 18.5 deliberate short runs states:
18.5 Deliberate short runs
18.5.1 If either umpire considers that one or both batsmen deliberately ran short at that umpire’s end, the umpire concerned shall, when the ball is dead, call and signal Short run and inform the other umpire of what has occurred and apply 18.5.2.
18.5.2 The bowler’s end umpire shall
- disallow all runs to the batting side
- return any not out batsman to his/her original end
- signal No ball or Wide to the scorers, if applicable
- award 5 Penalty runs to the fielding side
- inform the scorers as to the number of runs to be recorded
- inform the captain of the fielding side and, as soon as practicable, the captain of the batting side of the reason for this action.
In accordance with the rules, the umpire immediately made a signal to the scorers and also had a chat with both the fielding side and the two batsmen at the crease of the reason for the decision. As to why the five runs were added to the first innings and England didn't start the second at 5/0, Law 41 has the answer.
According to Law 41, which deals with unfair play and section 41.18, which covers penalty runs, it states:
41.18.4 When 5 Penalty runs are awarded to the fielding side, they shall be added as Penalty extras to that side’s total of runs in its most recently completed innings. If the fielding side has not completed an innings, the 5 Penalty runs shall be added to the score in its next innings.
In accordance with the rules, England's first innings total went from 285 to 290 after the five penalty runs were awarded.