What will happen if one column mentioned as primary key in DB and other column as primary key in mapping structure in informatica Powercenter or IICS.

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It would not create an issue, as long as it is for reading the data.

But, if we are going to write the data in the target(using different keys) then Informatica would perform the record operation(I/U/D) on the basis of the key defined in Informatica.