Testing Benchmarks
While this is one of the most popular pages hosted at the warehouse, we are planning to retire this tool. Upcoming changes will no longer collect some of the statistics required to continue updates. We apologize for any inconvenience.
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.
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.