My Sequence is Mostly Good, But There Are Some Problem Spots...

(section not yet written, but coming soon, including pictorial examples.)

(Actualy, much of this information is in another troubleshooting page, near the end: http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html)

• Spikes in the chromatogram (air bubbles on a dim chromatogram)
• A few peaks with multiple colors (PCR on polymorphic genomic region)
• The first few nucleotides are poor (typical - don't expect good sequence close to the primer)
• One base is [wrong/missing/inserted]. Did the sequencer screw up? (probably not, but sequence the other strand)
• There's an 'N' in the midst of otherwise good sequence (mis-spaced peaks and ABI's basecaller 'bug')
• what else?()