Answer to Part 1.1: What type of sequence are you analyzing the GC content for? Is there an intrinsic reason on why the GC content of these specific sequences would violate your genome-wide expectations? (-0.25)
Answer to Part 1.2: Is there anything interesting regarding the overrepresented sequences in these samples? Are they associated with a biologically relevant function? (-0.25)
Answer to Part 2: What is the rationale for keeping 15 samples? how many samples pass the suggested unique-read cutoff? Are you sure there's no inconsistent structure for any of the tissue triplicates? (-0.5)
Otherwise I have no complaints. Good job!
Code: 4.5/4.5 Answers: 2.5/3.5 Plots: 2/2 Report: 1/1 Total: 10/11