Table 3 Coverage and agreement measurements comparing Crossbow (CB) and SOAP/SOAPsnp (SS) to the genotyping results obtained by an Illumina 1 M genotyping assay in the SOAPsnp study
| Â | Â | Â | Â | Â | Â | (SS) | (CB) | ||
|---|---|---|---|---|---|---|---|---|---|
Illumina 1 M genotype | Sites | Sites covered (SS) | Sites covered (CB) | Agreed (SS) | Agreed (CB) | Missed allele | Other disagreement | Missed allele | Other disagreement |
Chromosome X | Â | Â | Â | Â | Â | Â | Â | Â | Â |
   HOM reference | 27,196 | 98.65% | 99.83% | 99.99% | 99.99% | NA | 0.004% | NA | 0.011% |
   HOM mutant | 10,737 | 98.49% | 99.19% | 99.89% | 99.85% | NA | 0.113% | NA | 0.150% |
   Total | 37,933 | 98.61% | 99.65% | 99.97% | 99.95% | NA | 0.035% | NA | 0.050% |
Autosomal | Â | Â | Â | Â | Â | Â | Â | Â | Â |
   HOM reference | 540,878 | 99.11% | 99.88% | 99.96% | 99.92% | NA | 0.044% | NA | 0.078% |
   HOM mutant | 208,436 | 98.79% | 99.28% | 99.81% | 99.70% | NA | 0.194% | NA | 0.296% |
   HET | 250,667 | 94.81% | 99.64% | 99.61% | 99.75% | 0.374% | 0.017% | 0.236% | 0.014% |
   Total | 999,981 | 97.97% | 99.70% | 99.84% | 99.83% | 0.091% | 0.069% | 0.059% | 0.108% |