"Reuben, you are my firstborn, Simeon and Levi are brothers, the scepter shall not depart from Judah, Zebulun shall dwell by the haven of the sea, Issachar is a strong donkey, Dan shall judge his people, Gad, a troop shall tramp upon him, bread from Asher shall be rich, Naphtali is a deer let loose, Joseph is a fruitful bough, Benjamin is a ravenous wolf. All these are the twelve tribes of Israel." (Genesis 49)
"And now your two sons, Ephraim and Manasseh, who were born to you in the land of Egypt before I came to you in Egypt, are mine; as Reuben and Simeon, they shall be mine. Your offspring whom you beget after them shall be yours, they will be called by the name of their brothers in their inheritance." (Genesis 48:5-6)
Jacob adopted Ephraim and Manasseh and said, "Let my name be named upon them, and the name of my fathers Abraham and Isaac; and let them grow into a multitude in the midst of the earth." (Genesis 48:16)
Ephraim and Manasseh were not born to Jacob, they were adopted by Jacob as his sons and received an inheritance in the land of Israel.
"by the border of Naphtali, from the east side to the west, one section for Manasseh, by the border of Manasseh, from the east side to the west, one section for Ephraim" (Ezekiel 48:4-5)
"The priests, the Levites — all the tribe of Levi — shall have no part nor inheritance with Israel; they shall eat the offerings of the LORD made by fire, and His portion. Therefore they shall have no inheritance among their brethren; the LORD is their inheritance, as He said to them." (Deuteronomy 18:1-2)
Israel's tithes belonged to the Levites, "Behold, I have given the children of Levi all the tithes in Israel as an inheritance in return for the work which they perform, the work of the tabernacle of meeting." (Numbers 18:21)
Twelve tribes belonged to Jacob, but the Levites belonged to God. "Thus you shall separate the Levites from among the children of Israel, and the Levites shall be Mine." (Numbers 8:14)
Counting the Levites, there are thirteen tribes.