In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, aneuploidy, and polyploidy?
For example would have normal whole genome sequencing techniques detected that humans have 46 rather than 48 chromosomes?
Maybe a better way to put this question would be as follows:
Given the whole genome sequence for humans and a belief that chimpanzee had 46 chromosomes would whole genome sequencing of the chimpanzee most likely say
1) Here are the sequences for those 46 and by the way there was material left over.
2) Here is the best representation of all the chimpanzee's DNA mapped onto 46 chromosomes.
3) Here are the sequences for those 46 and chimpanzee's appear to have 48 chromosomes.