Table 5.
The comparisons of call rates and concordance on HapMap samples for X chromosome SNPs
| Criterion | E (Error) | Item | GenCall (%) | GenoSNP (%) | M3 (%) | Mdep3 (%) |
|---|---|---|---|---|---|---|
| GenCall, GenoSNP, | < 50 | Call rate | 97.67 | 99.00 | 99.31 | 99.75 |
| M3, Mdep3 | Accuracy | 97.38 | 98.41 | 98.65 | 99.60 | |
| < 10 | Call rate | 97.77 | 99.01 | 99.32 | 99.76 | |
| Accuracy | 97.48 | 98.45 | 98.69 | 99.63 | ||
| < 1 | Call rate | 97.91 | 99.03 | 99.33 | 99.77 | |
| Accuracy | 97.63 | 98.49 | 98.72 | 99.65 |
Mdep3: the gender−dependent modified mixture model; M3: the modified mixture model; call rate: the percentage of valid genotypes; accuracy: the percentage of consistent genotype; criterion: which algorithm is selected to count E values between this algorithm and HapMap project due to the mis-assignment of major allele. E: the average error caused by the mis-assignment of the major allele under four criterions, GenCall, GenoSNP, M3 and Mdep3, and three E cutoffs, E < 50, 10 and 1 are set.