Table 1 Comparison of high confidence differences (HCDiffs) obtained from the CTRL and DEFA regions by sequence capture (SeqCap) with HapMap SNP genotypes.
| Â | NA12716 | NA12760 | Â | NA12716 | NA12760 |
|---|---|---|---|---|---|
HapMap: heterozygous | 244 | 263 | SeqCap: heterozygous | 711 | 646 |
SeqCap: | Â | Â | HapMap: | Â | Â |
homozygous for reference, no HCDiff | 0 | 5 | heterozygous | 237 | 248 |
homozygous for reference | 0 | 2 | homozygous for variant | 5 | 4 |
heterozygous | 237 | 248 | homozygous for reference | 10 | 4 |
homozygous for variant | 3 | 0 | Â | Â | Â |
not or poorly covered/alignment problem | 4 | 8 | Â | Â | Â |
HapMap: homozygous for variant | 254 | 217 | SeqCap: homozygous for variant | 526 | 468 |
SeqCap: | Â | Â | HapMap: | Â | Â |
homozygous for reference, no HCDiff | 0 | 0 | homozygous for variant | 248 | 212 |
homozygous for reference | 0 | 0 | homozygous for reference | 0 | 0 |
heterozygous | 5 | 4 | heterozygous | 3 | 0 |
homozygous for variant | 248 | 212 | Â | Â | Â |
not or poorly covered/alignment problem | 1 | 1 | Â | Â | Â |
HapMap: homozygous for reference | 839 | 842 | SeqCap: homozygous for reference | 151 | 137 |
SeqCap: | Â | Â | HapMap: | Â | Â |
homozygous for reference, no HCDiff | 827 | 835 | homozygous for variant | 0 | 0 |
homozygous for reference | 1 | 1 | homozygous for reference | 1 | 1 |
heterozygous | 10 | 4 | heterozygous | 0 | 2 |
homozygous for variant | 0 | 0 | Â | Â | Â |
not or poorly covered/alignment problem | 1 | 2 | Â | Â | Â |
Sensitivity (heterozygous) | 97,1% | 94,3% | Specificity (heterozygous) | 94,0% | 96,9% |
Sensitivity (homozygous) | 98,4% | 99,0% | Specificity (homozygous) | 98,4% | 98,6% |