We detected a mutation with a minor allele frequency (MAF) of 5.8% using NGS. However, the fractional abundance measured by ddPCR was significantly lower at 0.468575073 which represents a noticeable discrepancy between the two methods.

From the literature, I understand that a high concordance is generally expected between NGS and ddPCR for variant detection. Could anyone share insights or suggestions on what might be causing this discrepancy or how to approach resolving it?