Table 2.
Summary of the HapMap samples analyzed by each algorithm.
| Chip type | Training samples | Test samples |
|---|---|---|
| 550 k | 112 (48:12:16:36) | - |
| 650 k | 112 (48:12:16:36) | 15 (0:0:0:15) |
| 1 m | 118 (49:13:17:39) | 7 (3:0:0:4) |
| 370 k Duo | 115 (49:13:16:37) | 45 (30:0:0:15) |
| 1 m Duo | 269 (89:45:45:90) | 33 (11:3:2:17) |
| 370 k Quad | 225 (73:38:37:77) | - |
| 610 k Quad | 225 (73:38:37:77) | 27 (10:5:6:6) |
| 660 k Quad | 267 (88:44:45:90) | 47 (30:0:0:17) |
| omni1 Quad | 267 (88:44:45:90) | 67 (29:4:4:30) |
| Total | 1,710 | 241 |
The training samples were processed in-house by Illumina. The test samples were processed by an independent core facility. The number of samples from each of the four HapMap populations represented in each collection is given in parentheses (CEU:CHB:JPT:YRI).