Table 1 of
Yazar, Mol Vis 2013; 19:1238-1246. Table 1 of
Yazar, Mol Vis 2013; 19:1238-1246.
Table 1. Quality control details of genotyping in both cohorts.
| Cohort | Raine | BATS/TEST | BATS/TEST |
|---|---|---|---|
| Genotyping Centre | Centre for Applied Genomics (Toronto, Ontario, Canada) | deCODE (Iceland) | CIDR (USA) |
| Chip | Illumina 660 K | Illumina 610 K | Illumina 610 K |
| # genotyped SNPs (as supplied) | 657,366 | 592,392 | 589,296 |
| mean GenCall <0.7 | 95,876 | 47,418 | 36,877 |
| >5% missing | 1843 (97,719) | 8447 (47,950) | 12,455 (37,499) |
| p(HWE) <10-6 | 919 (98,449) | 2841 (49,616) | 15,474 (51,646) |
| MAF<0.01 (or monomorphic) | 23,370 (121,734) | 33,347 (69,632) | 28,607 (67,969) |
| # SNPs left | 535,632 | 529,379 | 531,042 |
| % genotyped SNPs | 81.48% | 89.36% | 90.11% |
| Dropout rate due to QIMR SNP QC | 18.52% | 10.64% | 9.89% |