I've been doing minipreps for close to 10 years using the standard qiagen kits and DH5a e. coli. I typically do 24 minipreps at a time and then identify the good plasmids by enzyme digestion, PCR, sequencing, etc. Something I've noticed is that the good plasmids often seemed to have higher DNA concentrations than the bad plasmids. I thought it was just superstition, but I looked back at a couple of recent miniprep batches and did statistics, and found that the good plasmids had a statistically significantly higher amount of DNA. I don't see this pattern all the time, but I have seen it when using InFusion based cloning and traditional restriction enzyme based cloning. I don't have access to all of my miniprep data, so I can't check everything for statistical significance.
So, why would "good" plasmids have better yields of DNA than "bad" plasmids? Has anyone else noticed this pattern?
As far as I knew, as long as the plasmid carried a working antibiotic resistance gene and the bacteria could replicate it efficiently, then the plasmid should be ok. Could the bad plasmids have been cases where the bacteria manages to ligate the vector backbone together but creates a sequence that doesn't replicate well? Could it be a timing issue, where the bad plasmid doesn't start replicating until later, so that the bacterial growth is delayed? I have not weighed the bacterial pellets, so I can't say anything about bacterial growth vs plasmid yield.