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Exploration will cover an area of 6,173 square kilometres (2,384 square miles) under the supervision of Qatar Petroleum, the company said.
It is JX Nippon's first exploration deal in Qatar where the Japanese firm is expected to make an initial investment of $100 million, it said at a ceremony to mark the signing of the agreement in Doha.
Qatar is the world's largest exporter of liquefied natural gas.