Why do I see "-/-" in reports? Why does my report say incomplete data?
This is normal with Whole Genome Sequencing, these are no-calls. When a data point fails our quality controls, that data point becomes a "no-call." We apply strict quality controls to prepare the raw data for analysis by our DNA analysis apps and reports, which helps ensure that only the highest quality data is analyzed. While the vast majority of data passes quality controls, there is a small percentage that fails.
Whole genome sequencing obtains data on ~100% of your genome. This means that the sequence of all genes and all chromosomes are obtained, making for a huge file compared to other platforms that provide genotyping services only. The files containing ~100% of your genome data, which are generated by the sequencing machines that sequenced your genome, are stored in two FASTQ files.
As the raw data is processed through Sequencing's bioinformatics pipeline (from FASTQ to BAM and then from BAM to VCF), we apply strict quality control checks to each and every data point throughout your genome, which means quality controls are applied to more than 3 billion data points.
So while the very raw data from the sequencing machine provides ~100% of your genome, there will always be some no-calls after our pipeline processes the data in preparation for the data to be analyzed by our apps and reports.
Other genome sequencing companies may not apply any quality controls to the data. Because of this, the processed data in the VCFs provided by those companies may look more complete because they have zero no-calls. But this is because there is no distinction between low quality data and high quality data. Without strict quality controls, the low quality data is included in their files.
Since Sequencing.com is focused on providing DNA analysis apps and reports that generate the highest quality analysis, we proactively exclude low quality data before the data is even analyzed by our apps and reports. This may be apparent when using apps that analyze a very large number of genetic variants throughout your genome, such as the Rare Disease Screen. Even when analyzing whole genome sequencing data, the results of this app usually have some data that is missing because those genetic variants being no-calls due to our strict quality controls.
Having no-calls in your whole genome sequencing data is expected and normal. As with all laboratory tests that look at many different data points, there will always be some random data points that don't pass quality control when the raw data is processed. This doesn't mean there is an issue with the test—on the contrary, there would only be an issue if 100% of the data points passed quality control because that's statistically not possible when a laboratory test is obtaining data on billions of data points.