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Garoppolo contract will be very difficult to negotiate

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Signing a long-term contract for quarterback Jimmy Grappolo will test the negotiating skills of 49ers’ lead negotiator Paarg Marathe and Garoppolo’s agent, Don Yee.

This is new territory for the team and Garoppolo. Players are hardly ever traded before their contracts are re-worked and Garoppolo has played brilliantly, but he’s only started seven NFL games. Then there’s the leverage of the franchise tag, which allows the 49ers to sign Garoppolo to one-year deals for the next two years.

Further complicating the issue is the 49ers’ desire to get out of any contract without heavily salary-cap implications. It means they like to sign players with as little guaranteed money as possible, and then they like to make the difference with incentives like playing time.

It’s one reason why they haven’t been an attractive free-agent destination. They also took advantage of Colin Kaepernick’s contract in their negotiations with players. When Kaepernick re-signed the last time, his signing bonus was only $16 million, while other quarterbacks around that time like Matt Ryan and Jay Cutler, received guaranteed money of twice that amount.

Many teams base their negotiating approach on how the contract of their highest paid player is structured. Consequently, the teams’s offers on extensions and free-agent deals were based on Kaepernick’s incentive-laden deal.

The team has softened on that somewhat. Wide receiver Pierre Garcon’s $47 million deal came with $20 million guaranteed. However, fullback Kyle Juszczyk received only $5 million of his $21 million contract in guarantees.

Guaranteed money is the only figure that makes sense in an NFL contract because most of them are back-loaded with high salaries that a team would never pay. However it makes the agent look good because it increases the overall value.

For example, nearly half of Garcon’s deal, $23.4 million, comes in salary in the last three years. But it’s unlikely Garcon will see the full $23.4 million and he might get any of it.

Then there’s the question of overall contract worth. Should Garoppolo be their fifth highest paid quarterback? The second? The seventh? And how do make that determination when he’s made only seven starts?

Further complicating the issue is the fact that there have been few quarterback contracts negotiated recently. Aaron Rodgers is the league’s highest paid quarterback with a five-year, $110 million deal with $54 million guaranteed, but that deal is nearly five years old. Because of its age, would Garoppolo want a similar contract? But would the 49ers give such a large sum to promising but unproven player?

All those questions will key negotiating points and their answers don’t have much precedence, which makes negotiating Garoppolo’s deal all the more difficult.