Q1. File "A": 66, File "B": 52
Q2. It has worked, but it seems that there wasnt enough data to produce a nice fit. We also only used a small subset of the entire dataset.
Q3. This looks better (blue vs. pink), but still the blue dots are not on a straight line around zero. 

If you want to see how it should look like:

acroread /home/local/27626/exercises/aln_process/bqsr_cycle.pdf &
acroread /home/local/27626/exercises/aln_process/bqsr_quality.pdf &
acroread /home/local/27626/exercises/aln_process/bqsr_dinuc.pdf &