Nope, there is no big difference between South-West and South-East Germany (Bavaria).
Slavic influence starts in Thuringia and is immediately very strong (already in Thuringia).
There is some Slavic influence in Obefranken, but it is not part of "historical Bavaria".
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Germany can be divided into three main genetic clusters:
- North-Western
- Southern (both SW and SE)
- Eastern (starts in Thuringia)
Thuringer Wald divides Eastern and Southern clusters:
https://upload.wikimedia.org/wikiped...inger_Wald.png
Border between NW and Eastern clusters is in Mecklenburg.