I have two plants, A and B (of the same diploid species).
I carried out a cross A x B, and ended up with progeny C.
I then mapped genomic sequencing reads (100bp) from a pool of DNA from 30 "C" progeny to plant B.
I also aligned genomic sequencing reads from plant A to plant B.
When I look at coverage of these genomic reads across transcript regions in plant B, I see that the coverage is generally less for the reads from plant A than for the reads from the pool of C plants.
One reason I can think of for this might be that half of the reads from a C plant will have the same SNP as one of the plant B alleles (at a heterozygous) site, whereas this might not be the case for reads from the unrelated plant A (resulting in fewer reads mapping across a transcript region as a whole).
However, my question is, regardless of genetic background, is there something integral to a pool of indviduals (something to do with condensed genomic regions or different regions being "harder" to sequence (or less likely to be sequenced) in each individual perhaps(?)) that means you will get a broader range of coverage from a pool individuals, than you would for a genomic sequencing run from a single individual?