when a clan was eradicated by their bitter enemies, how far down did the process of eradication reach?

now i understand that the daimyo of a losing clan, his immediate family and usually all his senior retainers would commit seppuku, retire to a monastery, or go into exile but how far down would that process go?

since the victor obviously coudn't depopulate the entire domain, was it just relegated to those who had had a personal relationship with the daimyo? or did it extend to the vassals of the senior retainers too or even further?

now i am sure a lot of that depended on the animosity between the two clans, but there must have been a point where further disenfranchisement of the lower class samurai would have been a negative gain to the victor in terms of lost administrators and warriors.

possible places where examples of this would be found would be in

Takeda vs Imagawa
Oda vs Asai
Toyotomi vs Akechi