Table 1.

Configuration Variables for Nucleotide Mixture Calling and Base “Marking” for Clinical Drug Resistance Genotyping.^22,23

Parameter	Value	Interpretation
Quality censoring cutoff	<10	Phred quality scores cut off for excluding bases during assembly.
Mixture area (%)	≥20	The area of the uncalled peak must be at least 20% of the called peak area. If 50% of the reads pass this threshold, then a mixture is called.
Mark area (%)	≥15	The area of the uncalled peak must have at least 17.5% of the called peak area. If ≥50% of the reads pass this threshold, then a mark is made.
Mark average quality cut-off phred score Additional marks	<20	If the average quality of the base across all reads is below the cutoff, then a mark is made. Insertions, deletions, and single primer coverage are also marked.