As part of our quality control process, an anonymized set of data is reviewed to ensure that it meets our quality standards prior to being loaded into your account. The data is reviewed for call rate and accuracy.
Call rate is defined as the fraction of called SNPs per sample over the total number of SNPs present on the genotyping chip. The vast majority of the variants on our chip have a 98% or greater call rate, meaning that the chip can provide data for more than 98% of those variants in any particular person. SNPs for which a confident determination cannot be made are reported as “no calls.” In the event that the overall call rate for a sample falls below our 98% threshold, the sample is subject to reanalysis.
Accuracy checks include, among others, comparing the genotype sex against the sex reported during registration.
Occasionally, sets or batches of samples are flagged for additional quality review. This does not reflect on the quality or viability of a particular sample, but simply the overall set of data. In order to ensure that you receive information that meets our standards, in these cases we will perform additional review steps prior to releasing data.