Table 5.
SNPs in each chip panel (SNPs after quality control) and samples used in the imputation
| SNP Chip | Number of SNPs (after QCa) |
Number of samples |
|---|---|---|
| Low density panel | ||
| GGP_8K | 8753 (7569) | 849 (325) |
| GGPLD-10 K-V2.0 | 9323 (7636) | 980 (424) |
| GGPLD-20 K-V1.0 | 20,701 (14,062) | 1189 (534) |
| GGPLD-20 K-V3.25 | 25,712 (18,786) | 1138 (374) |
| GGPLD-26 K-V3.0 | 26,728 (18,187) | 1344 (526) |
| GGPLD-30 K-V4.0 | 30,865 (20,560) | 1556 (1) |
| GGPLD-9 K | 8659 (6230) | 574 (6) |
| RefImp50k | ||
| LDMAX_SNPMap | 56,955 (39,736) | 3950 |
| ZM2_SNPMap | 60,911 (42,522) | 778 |
| GSTP_SNPMap | 54,609 (39,706) | 6673 |
| ZOE-50 K | 54,001 (37,231) | 231 |
| RefImpHD | ||
| GGPHD-770 K | 777,984 (587,437) | 1069 |
In low density arrays only the samples indicated in parenthesis were phenotyped for RFI. aQC: quality control