| Caller . | QC . | Monomorphic SNPs (of which rare misses) . | Mean r2 to manual calls . | ||||
|---|---|---|---|---|---|---|---|
| . | TP . | FP . | TF . | FF . | Sensitivity/specificity . | . | . |
| Illuminus | 1761 | 25 | 33 | 49 | 0.97/0.57 | 164 (21) | 0.993 |
| GenoSNP | 1668 | 2 | 56 | 142 | 0.92/0.97 | 85 (0) | 0.996 |
| GenCall | 1737 | 7 | 51 | 73 | 0.96/0.88 | 173 (1) | 0.997 |
| Optical | 1785 | 14 | 44 | 25 | 0.99/0.76 | 172 (0) | 0.997 |
| Manual | 1810 | 0 | 58 | 0 | 1.00/1.00 | 188 (0) | 1.000 |
| Caller . | QC . | Monomorphic SNPs (of which rare misses) . | Mean r2 to manual calls . | ||||
|---|---|---|---|---|---|---|---|
| . | TP . | FP . | TF . | FF . | Sensitivity/specificity . | . | . |
| Illuminus | 1761 | 25 | 33 | 49 | 0.97/0.57 | 164 (21) | 0.993 |
| GenoSNP | 1668 | 2 | 56 | 142 | 0.92/0.97 | 85 (0) | 0.996 |
| GenCall | 1737 | 7 | 51 | 73 | 0.96/0.88 | 173 (1) | 0.997 |
| Optical | 1785 | 14 | 44 | 25 | 0.99/0.76 | 172 (0) | 0.997 |
| Manual | 1810 | 0 | 58 | 0 | 1.00/1.00 | 188 (0) | 1.000 |
Monomorphic SNPs = the number of SNPs a genotype-calling algorithm calls monomorphic from its TPs, with the subset of missed rare variants (when compared to manual calls) shown in brackets. r2 is as in Section 3.1 and is calculated over the true QC pass SNPs which were polymorphic according to both the caller and the manual calls.
| Caller . | QC . | Monomorphic SNPs (of which rare misses) . | Mean r2 to manual calls . | ||||
|---|---|---|---|---|---|---|---|
| . | TP . | FP . | TF . | FF . | Sensitivity/specificity . | . | . |
| Illuminus | 1761 | 25 | 33 | 49 | 0.97/0.57 | 164 (21) | 0.993 |
| GenoSNP | 1668 | 2 | 56 | 142 | 0.92/0.97 | 85 (0) | 0.996 |
| GenCall | 1737 | 7 | 51 | 73 | 0.96/0.88 | 173 (1) | 0.997 |
| Optical | 1785 | 14 | 44 | 25 | 0.99/0.76 | 172 (0) | 0.997 |
| Manual | 1810 | 0 | 58 | 0 | 1.00/1.00 | 188 (0) | 1.000 |
| Caller . | QC . | Monomorphic SNPs (of which rare misses) . | Mean r2 to manual calls . | ||||
|---|---|---|---|---|---|---|---|
| . | TP . | FP . | TF . | FF . | Sensitivity/specificity . | . | . |
| Illuminus | 1761 | 25 | 33 | 49 | 0.97/0.57 | 164 (21) | 0.993 |
| GenoSNP | 1668 | 2 | 56 | 142 | 0.92/0.97 | 85 (0) | 0.996 |
| GenCall | 1737 | 7 | 51 | 73 | 0.96/0.88 | 173 (1) | 0.997 |
| Optical | 1785 | 14 | 44 | 25 | 0.99/0.76 | 172 (0) | 0.997 |
| Manual | 1810 | 0 | 58 | 0 | 1.00/1.00 | 188 (0) | 1.000 |
Monomorphic SNPs = the number of SNPs a genotype-calling algorithm calls monomorphic from its TPs, with the subset of missed rare variants (when compared to manual calls) shown in brackets. r2 is as in Section 3.1 and is calculated over the true QC pass SNPs which were polymorphic according to both the caller and the manual calls.
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