Capture Quality Control

Input parameters
File Number reads % target bases with
coverage >= 1.0x
Coverage saturation
(slope at the end of the curve)
% reads on target Duplicated reads
on/off target
Coverage distribution
(mean coverage)
Coverage per position Standard deviation of
coverage within regions
/home/user/ngsCAT/example2.bam 237535 51.1% 4.6e-05 67.3% ON-25.7%; OFF: 8.1% 31.8x 8207 consecutive bases
with coverage <= 6
Overall status


Please, note that the criteria to decide whether a particular experiment was successful, or not, are dependent on the capture design, sequencing platform and data analysis pipeline. The default warning thresholds are based on general whole exome enrichment experiments. If these default thresholds are not appropriated for your experiment, they can be modified by editing the configuration file As a general guideline, sensitivity parameters are more relevant than specifity parameters and the latter more than uniformity ones according to their impact in the performance of target enrichment experiments

Sensitivity A set of graphs and data tables that allow to assess how well those bases in the target regions were sequenced.
Specificity A set of graphs and data tables that allow to assess how much of the sequencing effort is being wasted in sequencing off-target regions.
Uniformity Set of graphs and data tables that allow to assess whether coverage is uniformly distributed among target regions.