Table 1 Concordance between Birdseedv2 and consensus HapMap calls of 34,922 genotypes
From: Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
HapMap Call | Birdseedv2 call | |||||||
|---|---|---|---|---|---|---|---|---|
| Â | Original | Spatial normalization | ||||||
| Â | 0 | 1 | 2 | Missing | 0 | 1 | 2 | Missing |
0 | 3356 (9.6) | 2002 (5.7) | 19 (0.05) | 7045 (20.2) | 7451 (21.3) | 960 (2.7) | 11 (0.03) | 4000 (11.5) |
1 | 496 (1.4) | 2040 (5.8) | 550 (1.6) | 4257 (12.2) | 393 (1.1) | 4340 (12.4) | 428 (1.2) | 2182 (6.2) |
2 | 17 (0.05) | 2157 (6.2) | 3470 (9.9) | 7343 (21.0) | 14 (0.04) | 1135 (3.3) | 7614 (21.8) | 4224 (12.1) |
Missing | 322 (0.92) | 627 (1.8) | 323 (0.92) | 898 (2.6) | 300 (0.86) | 575 (1.6) | 311 (0.89) | 984 (2.8) |