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Q: What is the depth for individual re-sequencing and population re-sequencing?

A: 10~30X depth for individual re-sequencing and 5~10× depth for population re-sequencing are recommended. If a higher accuracy requirement for SNP detection of a complex genome species , a higher sequencing depth is necessary.

 

Q: How sweeps to be categorized ?

A: The "classic selective sweep" or "hard selective sweep" is expected to occur when beneficial mutations are rare, but once a beneficial mutation has occurred its increases in frequency rapidly, thereby drastically reducing genetic variation in the population.

 A so-called "soft sweep from standing genetic variation" occurs when a previously neutral mutation that was present in a population becomes beneficial because of an environmental change. Such a mutation may be present on several genomic backgrounds so that when it rapidly increases in frequency, it doesn't erase all genetic variation in the population.

Finally, a "multiple origin soft sweep" occurs when mutations are common (for example in a large population) so that the same or similar beneficial mutations occurs on different genomic backgrounds such that no single genomic background can hitchhike to high frequency.