Table 2. Similar to Table 1, but without applying the error model to the simulated true genotypes of sampled individuals.

		RABBIT
Probability	Simulated data set	JointModel	indepModel	depModel	GAIN	HAPPY (diploid)	HAPPY (haploid)
Wrongly assigned	MAGIC-F5	0.132	0.132	0.935	NA	0.690	0.943
	MAGIC-F11	0.095	0.132	0.105	NA	0.324	0.239
	CC-F11-AA	0.024	0.031	0.209	0.030	0.139	0.225
	CC-F22-AA	0.023	0.033	0.045	0.028	0.079	0.068
	CC-F11-XX	0.012	0.015	0.185	0.018	0.105	0.194
	CC-F22-XX	0.011	0.015	0.028	0.016	0.043	0.041
Wrongly called	MAGIC-F5	0.098	0.098	0.934	NA	0.178	0.936
	MAGIC-F11	0.073	0.114	0.084	NA	0.151	0.097
	CC-F11-AA	0.017	0.024	0.205	0.017	0.039	0.210
	CC-F22-AA	0.017	0.027	0.040	0.016	0.040	0.045
	CC-F11-XX	0.008	0.011	0.182	0.008	0.023	0.186
	CC-F22-XX	0.007	0.012	0.026	0.007	0.020	0.029
Pedigree inconsistency	CC-F11-AA	0.00057	0.0034	0	0	0.020	0
	CC-F22-AA	0.00011	0.0032	0	0	0.009	0
	CC-F11-XX	0.00021	0.0012	0	0	0.015	0
	CC-F22-XX	0.000054	0.0014	0	0	0.005	0