Problem statement:

I have to analyze a illumina paired end data for a 5kb genomic region from rice(japonica) and I am interested to detect the variations in a gene in my 5 different transgenic rice lines. I have one sample sequenced from each line. The sequencing was done using the Sbs-SeqCap method.

Questions:

1. What more information do I need from the wet lab side to do the analysis?
2. I want to understand the variation in all the regions (promoter, cds, terminator etc) in the gene in all different lines. More the information I can capture, better it is. what would be the workflow?
3. Do I just need to run the variant calling workflow? I guess I can do more than that with this data.

This is to get an opinion about the various ways I can approach this problem.

Thanks in advance