The following sources may contribute to DNA yields after Library PCR that are below the recommended specifications (e.g., 2 ng/µL):
| Source | Recommended Steps |
| Low template concentration | Verify that the DNA concentration of the 1st PCR is correctly quantified. Repeat the Library PCR with increased cycles of up to 12. |
| Wrong primer concentration | Verify that each sample is amplified with 10 µL of Index Primer Pair. |
| Wrong thermal cycling protocol | Ensure that the correct thermal cycling protocol conditions are used, including temperature and cycle number. |
These may occur alone or in combination.