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Trace File Failures
The quality of trace files can vary considerably, but most traces will contain both high and low quality sections. Deciding when a trace file should be discarded can be a difficult decision. The following cases highlight when it is appropriate to discard a trace file.
Case 1: Poor Quality DNA
When the DNA used to generate a trace file is low quality, the peaks are often too ambiguous to call bases and the sequence cannot be corrected.
Case 2: Complete Lack of DNA Amplification
Complete lack of amplification can occur when there is no PCR product in the sequencing reaction or the sequence reaction failed.
Case 3: Contamination and Co-amplification of Unrelated Sequences
If two or more sequences from unrelated species are co-amplified, double-peaks will be present at almost every base position.
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