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NotIn order for something to constitute a clause, it is required to have a finite form of a verb. As there are a lot of scenarios where there is a comma, but not two finite verbs, not every comma creates a subordinate(subordinate) clause. Here are just a few constructions with a comma and no subordinate clause, this is not necessarily a complete list:

  1. Some commas are just enumerations:

Ich gehe zum Bäcker, nach Hause, und danach ins Büro.

  1. Another common counterexample of your hypothesis is a paratactic structure, that is two main clauses connected by a conjunction. Conjunctions of und, oder, and denn, (and others probably, this is just off the top of my head) combine two main clauses:

Ich gehe zum Bäcker und danach gehe ich nach Hause. 
Ich gehe zum Bäcker oder ich gehe ins Büro. 
Ich gehe zum Bäcker, denn ich habe Hunger.

There is a lot more on this, and I recommend you read a grammar introduction into main clauses and subordinate clauses in German. Maybe [this]1 could be a good start.

  1. A third example is an apposition:

Monika Meyer, unsere Direktorin, ist heute im Urlaub.

  1. Another group (and this is the one in your example), is just an interjection:

Ja, du hast das wohl gemacht.

[Ja,] cannot be a clause, because it has no finite verb.

Not every comma creates a subordinate clause. Here are just a few constructions with a comma and no subordinate clause, this is not necessarily a complete list:

  1. Some commas are just enumerations:

Ich gehe zum Bäcker, nach Hause, und danach ins Büro.

  1. Another common counterexample of your hypothesis is a paratactic structure, . Conjunctions of und, oder, denn, (and others probably, this is just off the top of my head) combine two main clauses:

Ich gehe zum Bäcker und danach gehe ich nach Hause. Ich gehe zum Bäcker oder ich gehe ins Büro. Ich gehe zum Bäcker, denn ich habe Hunger.

There is a lot more on this, and I recommend you read a grammar introduction into main clauses and subordinate clauses in German. Maybe [this]1 could be a good start.

  1. A third example is an apposition:

Monika Meyer, unsere Direktorin, ist heute im Urlaub.

  1. Another group (and this is the one in your example), is just an interjection:

Ja, du hast das wohl gemacht.

[Ja,] cannot be a clause, because it has no finite verb.

In order for something to constitute a clause, it is required to have a finite form of a verb. As there are a lot of scenarios where there is a comma, but not two finite verbs, not every comma creates a (subordinate) clause. Here are just a few constructions with a comma and no subordinate clause, this is not necessarily a complete list:

  1. Some commas are just enumerations:

Ich gehe zum Bäcker, nach Hause, und danach ins Büro.

  1. Another common counterexample of your hypothesis is a paratactic structure, that is two main clauses connected by a conjunction. Conjunctions of und, oder and denn (and others probably, this is just off the top of my head) combine two main clauses:

Ich gehe zum Bäcker und danach gehe ich nach Hause. 
Ich gehe zum Bäcker oder ich gehe ins Büro. 
Ich gehe zum Bäcker, denn ich habe Hunger.

There is a lot more on this, and I recommend you read a grammar introduction into main clauses and subordinate clauses in German. Maybe [this]1 could be a good start.

  1. A third example is an apposition:

Monika Meyer, unsere Direktorin, ist heute im Urlaub.

  1. Another group (and this is the one in your example), is just an interjection:

Ja, du hast das wohl gemacht.

[Ja,] cannot be a clause, because it has no finite verb.

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Not every comma creates a subordinate clause. Here are just a few constructions with a comma and no subordinate clause, this is not necessarily a complete list:

  1. Some commas are just enumerations:

Ich gehe zum Bäcker, nach Hause, und danach ins Büro.

  1. Another common counterexample of your hypothesis is a paratactic structure, . Conjunctions of und, oder, denn, (and others probably, this is just off the top of my head) combine two main clauses:

Ich gehe zum Bäcker und danach gehe ich nach Hause. Ich gehe zum Bäcker oder ich gehe ins Büro. Ich gehe zum Bäcker, denn ich habe Hunger.

There is a lot more on this, and I recommend you read a grammar introduction into main clauses and subordinate clauses in German. Maybe [this]1 could be a good start.

  1. A third example is an apposition:

Monika Meyer, unsere Direktorin, ist heute im Urlaub.

  1. Another group (and this is the one in your example), is just an interjection:

Ja, du hast das wohl gemacht.

[Ja,] cannot be a clause, because it has no finite verb.