Ground Ball Thrown out of Play

 
With runners on first base (R1) and third base (R3), R1 is stealing on the pitch. The batter (B1) hits a grounder deep to the shortstop. Shortstop has no play on R1 at second base, so he throws home to attempt to retire R3. The throw bounces in the dirt, hits the catcher's shin guard and ricochets into the dugout.
 
At the time of the shortstop's throw (and also at the time the ball rolled into the dugout), R1 had reached second base but the batter was only halfway to first base.
 
Where do the umpires place R1 and B1?
 
Call
The ball becomes immediately dead when a thrown ball goes into dead ball territory (NF 5-1-1g2).
 
When the first throw by an infielder goes out of play, each runner (including the batter-runner) is awarded two bases -- determined from their position at the time of the pitch (NF 8-2 and 8-3-3c).
 
In the situation below, at the time of the pitch, R1 was at first base and R3 was at third base, so R3 scores, R1 is awarded third base, and the batter is awarded second base.