Testing Benchmarks

Mean NGS Callable Coverage by Test Type
Callable Loci Poor Alignment Total Loci Samples (n) Est. Years/SNP
Vendor Test Type Avg CV Avg CV Avg CV

Explanation of Metrics

The coverage table is produced using BWA-MEM aligned BAMs on the GRCh38 reference genome. The BAMs are processed by GATK's CallableLoci tool with default settings. For a location to be considered callable it must have four reads overlapping the site. No more than ten percent of those reads may have a PHRED-scaled alignment quality of less than 10. Yielding a heuristic combined quality indicating less than 0.01% chance all the reads are aligned incorrectly to the site.

Callable - The total number of sites sequenced with 4 or more reads. Each read has less than 10% likelihood of being misaligned.

Poor Alignment - The sites having more than four reads, but the aligner indicates a high likelihood the results may not be correct.

Samples (n) - The size of the population who have submitted BAMs for this type of test. The numbers are self-selected and likely bear little resemblance to actual market size.

Est. Years/SNP - This figure applies a mutation rate of 8.2e-10 per year per bp to the Callable Loci statistic. The constant is sourced from Poznik et al. (2013)

Total Loci - The sites having at least one read assigned. This metric is less useful when looking at a sample in isolation, but can be useful when looking at the population as a whole. The PAR regions are not included in these statistics as they are treated as part of the X chromosome due to recombination.