Pipeline sensitivity and precision

Variant Type	Measure	Sensitivity	Precision	Truth set
Single Nucleotide Variants	Mean	0.9978	0.9995	HG002 (high confidence regions)
Single Nucleotide Variants	95% credible interval	0.9978-0.9979	0.9995-0.9995	HG002 (high confidence regions)
Indels	Mean	0.9979	0.9991	HG002 (high confidence regions)
Indels	95% credible interval	0.9977-0.9980	0.9990-0.9991	HG002 (high confidence regions)
Copy Number Variants (>2Kb)	Mean	0.9779	N/A	Clinically significant CNVs detected by standard of care tests in accredited labratories
Copy Number Variants (>2Kb)	95% credible interval	0.9609-0.9929	N/A	Clinically significant CNVs detected by standard of care tests in accredited laboratories
Short Tandem Repeat Expansions	Mean	0.9828	0.9194	STR expansion tests (positive and negative) at target loci performed in accredited laboratories
Short Tandem Repeat Expansions	95% credible interval	0.9343-1	0.8252-0.9943	STR expansion tests (positive and negative) at target loci performed in accredited laboratories

Note

HG002: (Child, Ashkenazi Jewish Trio) sample with Genome in a Bottle truth set (high confidence regions) - metrics reported here relate to variant detection performed as a singleton