Jones started play on the back nine, was one over at the turn and still on track to make the cut with five holes to play.
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But bogeys on the fourth and fifth holes and a double bogey on the sixth saw him drop back in the field and miss the cut by three strokes with his total of 11-over-par.
Jones entered the championship knowing the first six holes had the reputation of being the toughest six holes in US Open history, and while he navigated them reasonably well on the first day of play, with one double bogey, it proved his downfall today as he went through the same stretch at four over.
Despite today’s poor finish, Jones was still ruing his disappointing opening round where he played well but made some costly mistakes.
“The damage was done yesterday,” Jones said after missing the cut with the late bogeys, noting that missing fairways in the run home “made it tough.”
Overnight leader, Michael Thompson dropped back to equal second at one over after carding five over today, with Tiger Woods now sharing the lead with Jim Furyk and David Toms at one under.
Alistair Presnell carded four over today but is still the leading Australian in the field, five shots off the pace.
He will join fellow countrymen John Senden, Adam Scott, Jason Day and Rod Pampling in the third round tomorrow.
Geoff Ogilvy, Aaron Baddeley Anthony Summers all missed the cut, as did defending champion Rory McIlroy.