Table 3.
Genotype discordances between original genotypes and imputed genotypes (Dataset A: 204 samples)
| SNP | rs1997375 | rs10250847 |
|---|---|---|
| No. of calls | 204 | 204 |
| No. of AB calls imputed to be AA or BB | 41 | 0 |
| No. of AA or BB calls imputed to be AB | 4 | 0 |
| No. of AA or BB calls imputed to be BB or AA | 3 | 0 |
| No. of total genotype discordances | 48 | 0 |
The table contains a summary of genotype comparisons between the original genotype calls and the Beagle 3.0-imputed genotype calls for the top two genome-wide significant SNPs. The top SNP (rs1997375) displays many (48) discordances in total. However, the second SNP (rs10250847) does not, lending evidence towards it being a stronger hit.