Troubleshooting

A small amount of background noise is always present in sequencing data. Noise is characterised by high background and peaks under peaks causing ambiguities in basecalling. Noise can either be found throughout the sequence data or after a specific point in the sequence.

Noise throughout the sequence can be caused by:

• Very low signal strength
• High signal strength causing the detector to become saturated
• Contaminated template
• Multiple templates in the sequencing reaction
• Multiple priming sites
• Multiple primers
• No primer

Noise after a point in the sequence can be caused by:

• Mixed plasmid or PCR prep
• Frameshift mutation
• Repeat region in the template
• Slippage after a homopolymer region in the template
• Primer-dimer contamination