If humans have 46 chromosomes, then why are Haplogroups only based on Y-chromosome? What about the other 45?

As far as i understand, Haplogroups trace our ancestry by our y-chromosome and mitDNA. But what about the other 45 chromosomes? Also, since we humans share 99.4 percent identical genes, does that mean, the y-chromosome differences are the other 0.6 percent of our DNA? Also, why are there so many different kinds... show more As far as i understand, Haplogroups trace our ancestry by our y-chromosome and mitDNA. But what about the other 45 chromosomes?

Also, since we humans share 99.4 percent identical genes, does that mean, the y-chromosome differences are the other 0.6 percent of our DNA?

Also, why are there so many different kinds of haplogroups? Do they all make up the remaining 0.6 percent of our DNA?

Why aren't there various types of mitDNA like there are for y-chromosomes?
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