TABLE 1

Variant detection sensitivity as a function of the threshold in Phred-like quality score

StrainCoverageSensitivity (%)quality >20Sensitivity (%)quality >30Sensitivity (%)quality >40
VC236611.9×78.678.564.5
VC236212.7×83.884.276.7
VC192312.8×81.781.973.7
RB500014.0×88.789.387.6
DM101716.0×87.587.582.9
VC245120.3×90.891.287.4
VC245223.0×90.491.287.6
VC192423.4×95.195.793.2
RB500229.1×94.795.195.1
RB500130.1×93.493.994.2
  • The variant detection sensitivity was evaluated for individual strains using three different thresholds in Phred-like quality score from Maq. Variants common to VC2010 and WU N2 were used for the evaluation, and the list comprised 655 variants at quality >20, 634 variants at quality >30, and 533 variants at quality >40.