I am planning to sequence some genomic DNA with NGS and as a control/estimation of error in my workflow, I plan to spike in a synthetic oligo of ~100 bp (plus adaptors). At the center of it will be my "base+probe" which I am interested in. 10 bases on either side of the probe will be mixed bases (25% probability for each). The remaining 79 bases will then be known. I wanted to ensure that this is feasible having these mixed bases in NGS and that I can pinpoint the probe (will be read as a specific base) in the center of them.
Thanks in advance.