Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Table 2
Performance of add-on tags, categorized based on settings and methods.
Number of probes (Column 2) indicates the total number of Illumina probes that are required to genotype the add-on tags. The mean probe-ability score (Column 3) estimates the genotyping success rate for the selected add-on probes. The number of successfully tagged imputed variants are measured by either any improvement in INFO score (Column 4), or those exceeding INFO score of 0.8 when previously below (Column 5). Per probe and per tag indicate the number of imputed variants with imputation improvements per add-on tag and add-on probe respectively. Standard error (SE) represents variability of the per tag and per probe metric across different genomic regions. %AFGR and %Tanz indicate the proportion of imputed variants with better imputation accuracy based on the AFGR or internal Tanzanian reference panel respectively.