So I'm quite new to GBS data and have been given a dataset for analysis. The Proso millet genome was sequenced. There are 3 samples - one wild type/control and two mutants, one high yielding and one low yielding mutant.
This is what has been previously done: Non-synonymous, stop gain and stop loss SNPs were identified between wild and mutants. Using NCBI search in the sequence data of the crop (Proso millet), the info about genes corresponding to these SNPs were identified. The Uniprot pathway mapper was used where one SNP was detected in the starch synthase pathway.
What other analysis could I perform using this data to identify anything with regards to SNPs or gene expression? I understand that GBS coverage is quite low compared to whole genome.. Any input would be appreciated! :)