Assembled Contig Without GOI?? Seriously??

It has been a while since I posted the last activity. It is because I was extremely down to receive the news that the nanopore sequencing result of pE2-MaSpCL did not yield any positive result. So, I kept the result without doing detail analysis until yesterday. When my mind was in a stable state, I continued comparing the sequence contig generated with the empty plasmid and surprisingly, I found that the entire contig was actually made of the vector backbone!. However one thing for sure, the hundred basepairs upstream and downstream region to the MSC supposedly containing the insert were missing. How did this happen? I have no idea at all. It seems that the sequencing has faced difficulty in reading out the insert containing repetitive regions in long read...After discussing with my SV, I was told to resort to the conventional way via primer walking.. Gosh...

 

Only the green color were present in the contig while the unshedded part including the MSC site was missing from the contig...