The SB paused a long time before checking here, I initially thought that he must have flopped a big draw or two pair, for some reason I still fired a cbet, bad idea!

PokerStars No-Limit Hold'em, $0.25 BB (5 handed) from (Format: FlopTurnRiver)

BB ($10.25)
UTG ($28.90)
MP ($32.60)
Hero ($40.60)
SB ($12.95)

Preflop: Hero is Button with J, 9.
UTG calls $0.25, 1 fold, Hero raises to $1.25, 1 fold, BB calls $1, UTG calls $1.

Flop: ($3.85) Q, J, A (3 players)
BB checks, UTG checks, Hero bets $2.9, BB calls $2.90, UTG calls $2.90.

Turn: ($12.55) T (3 players)
BB checks, UTG checks, Hero checks.

River: ($12.55) 6 (3 players)
BB bets $6.1 (All-In), UTG calls $6.10, Hero folds.

Final Pot: $24.75

I don't know, people pause for a long time for like 1134502347529 reasons. Maybe they are multitabling, maybe they are thinking about bluffing, who knows. I generally ignore this. You are heads up, you raised, and it was checked to you in position. Other than a possible timing tell, how do you know your opponent has a piece? Meh, I dunno. I'm betting there most of the time.