Table 4 Concordance between Birdseedv2 and non-redundant HapMap calls of 261,267 genotypes
From: Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
HapMap | Birdseedv2 call | |||||||
|---|---|---|---|---|---|---|---|---|
Call | Original | Spatial normalization | ||||||
| Â | 0 | 1 | 2 | Missing | 0 | 1 | 2 | Missing |
0 | 27,735 (10.6) | 14,592 (5.6) | 233 (0.09) | 43,806 (16.8) | 48,341 (18.5) | 9,925 (3.8) | 168 (0.06) | 27,932 (10.7) |
1 | 6,324 (2.4) | 21,250 (8.1) | 6,147 (2.4) | 38,035 (8.1) | 5,483 (2.1) | 43,252 (16.6) | 5,558 (2.1) | 17,463 (6.7) |
2 | 186 (0.07) | 15,162 (5.8) | 27,250 (10.4) | 44,576 (17.1) | 169 (0.06) | 10,073 (3.9) | 48,807 (18.7) | 28,125 (10.8) |
Missing | 2,183 (0.84) | 4,287 (1.6) | 2,350 (0.90) | 7,151 (2.7) | 3,007 (1.2) | 5,034 (1.9) | 3,108 (1.2) | 4,822 (1.8) |