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DP83TG720R-Q1: Register setting

Part Number: DP83TG720R-Q1

Hi team,

We are referring to SNLA371A.pdf and Linux driver file, dp83tg720.c. 
And they have some differences on register setting. Which one do we need to refer to for OA TC12 test?

Do we have to refer to the app note(MUST) or if we get problems on using .c code, we may refer to the app note(CAN)?

Best regards,
Yuto