In this file photo, construction workers with Capital Rail Constructors make adjustments to a girder on the Dulles extension of the Silver Line of the Metro on  April 21, 2015. (Photo by Pete Marovich For The Washington Post)

Last spring officials announced that the second phase of the Silver Line rail project was behind schedule. Now, nearly a year later, we’re learning just how costly that 13-month delay will be.

Officials at the Metropolitan Washington Airports Authority have paid Capital Rail Constructors, the lead contractor on the $5.6-billion rail project, $40 million dollars to compensate for the delay, which forced the company to halt design work and construction. The hold up was blamed in part for design changes associated with storm water management to meet new federal and state requirements. The rule change required contractors to redesign the entire 11.4-mile portion of the rail line’s second phase.

Charles Stark, executive director of the rail project, said the bill likely will go higher as the two sides negotiate a settlement. And that doesn’t take into account other costs. In all, there have been more than 150 design changes associated with rail line’s second phase. So far those change orders and directive letters have added an addtional $9.3 million to the project’s cost.

The increased costs will be covered by the project’s $551.5 million contingency fund, which as of November had $477 million remaining. Officials have spent roughly $74.5 million– or 13 percent–of the money set aside to cover overages and Stark told members of MWAA’s board of directors Wednesday he still expects to complete the project within budget.

The first phase of the Silver Line, which opened in July 2014, was more than $220 million over budget and opened six months late. The first phase included five stops — four in Tysons Corner and one in Reston. The second phase will have six stops — including one at Dulles International Airport and two in Loudoun County.

Although the rail line is being built by MWAA, it will be operated by Metro.

The first phase was built by Dulles Transit Partners, which was led by construction giant Bechtel. Jack Potter, MWAA’s president and chief executive officer, said last spring that the authority was close to reaching a financial agreement with Bechtel to cover outstanding work and settle remaining bills. At the time, Potter said the authority preferred to settle rather than engage in a costly fight with the contractor. He noted that any settlement with Bechtel would not be made public. However, board documents released late last year, indicate that Bechtel received $45.9 million as part of a “contract close-out.”

Another contractor was hired to complete some of the outstanding work.