What can you do with whole genome sequecing by illumina of a crop population

Question

[Hann]

Dear all,

I have whole-genome sequencing of 150 individuals of a crop species and 14 individuals of its wild relative, produced by Illumina short reads sequencing.

We have done SNP calling and looked at the evolutionary history (i.e., diversity, structure, effective population size, GWAS ...etc)

Based on SNPs we have also investigated genomic footprints of selection and domestication

I wonder what are the other things you can answer from short Illumina reads sequencing rather than using SNPs for different analyses

I want to make the use of this source of data, but I don't know how and what to do?!

Any comments!?

[cschu181]

I assume you have called against a common reference? Maybe, especially for the wild relative individuals, see what/how many reads didn't align and maybe assemble them, given high enough coverage.