‘And Jacob said to Joseph, “El Shaddai (God Almighty) appeared to me at Luz in the land of Canaan, and blessed me, and said to me, ‘Behold I will make you fruitful and multiply you, and I will make of you a company of peoples and will give this land to your seed for ever for an everlasting possession.' And now your two sons, who were born to you in the land of Egypt before I came to you into Egypt, are mine, Ephraim and Manasseh, even as Reuben and Simeon shall be mine. And your issue, which you have begotten after them, shall be yours. They shall be called after the name of their brothers in the inheritance.”
The repetition of the covenant appearance is important (see Genesis 35:11-12). Jacob wants it to be clear that Joseph's two sons, born in Egypt, are not excluded from the covenant and the promises, for the promise was given by El Shaddai, lord of the whole earth. So he now intends to adopt the two children of Joseph giving them the rights of full sons, on equality with Reuben and Simeon. (He is speaking to Joseph. He is not aware at this moment that they are standing there behind Joseph).
“And your issue (Ephraim and Manasseh) which you have begotten after them (Reuben and Simeon) shall be yours.” That is they will stand in Joseph's place in the inheritance.
The mention of Ephraim before Manasseh is deliberate. Jacob knows what he is about to do.