I have the following:

• SAMPLE 1: a culture of normal unmodified HEK293 cells (a pure population where all cells are the same)
• SAMPLE 2: a culture of HEK293 cells on which I did a custom gene knock in via CRISPR and homology directed repair. (after a 90%+ transfection rate, only about 3% of cells sustained a stable knock-in as indicated by the GFP sequence i stuck on the end of my gene (which was designed to be knocked-in along with the gene))

I was told I could submit both samples to be sequenced and that NGS targeted sequencing / amplicon sequencing would be able to confirm whether or not my donor gene was inserted at my desired target sites. Is this correct?

(considering that sample 2 is a mixed population and only about 3% exhibit what appears to be a stable knock-in)