Table 2 Similar to Table 1, but without applying the error model to the simulated true genotypes of sampled individuals
RABBIT
ProbabilitySimulated data setJointModelindepModeldepModelGAINHAPPY (diploid)HAPPY (haploid)
Wrongly assignedMAGIC-F50.1320.1320.935NA0.6900.943
MAGIC-F110.0950.1320.105NA0.3240.239
CC-F11-AA0.0240.0310.2090.0300.1390.225
CC-F22-AA0.0230.0330.0450.0280.0790.068
CC-F11-XX0.0120.0150.1850.0180.1050.194
CC-F22-XX0.0110.0150.0280.0160.0430.041
Wrongly calledMAGIC-F50.0980.0980.934NA0.1780.936
MAGIC-F110.0730.1140.084NA0.1510.097
CC-F11-AA0.0170.0240.2050.0170.0390.210
CC-F22-AA0.0170.0270.0400.0160.0400.045
CC-F11-XX0.0080.0110.1820.0080.0230.186
CC-F22-XX0.0070.0120.0260.0070.0200.029
Pedigree inconsistencyCC-F11-AA0.000570.0034000.0200
CC-F22-AA0.000110.0032000.0090
CC-F11-XX0.000210.0012000.0150
CC-F22-XX0.0000540.0014000.0050