|Callable Loci||Poor Alignment||Total Loci||Samples (n)||Est. Years/SNP|
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.