Accuracy versus drop rate plots for the four methods tested for X chromosome SNPs. Results are shown for all samples (A), males only (B) or females only (C) from the 610 k Quad training data and all samples (D), males only (E) or females only (F) from the 610 k Quad test data respectively. Methods with separate models for male and female samples (Illuminus and CRLMM) are generally more accurate than methods which use the same model for both sexes (GenCall, GenoSNP). Performance of Illuminus in the test data set is worse than the other three methods despite the sex-specific model. Again this is due to small sample size. In the training data set there were 121 males and 104 females, and in the test data set there were 13 males and 14 females.