Table 3 Bias and MSE of mapgd, VCFtools, KING, and PLINK in estimating coancestry, fraternity, and inbreeding for outbred and inbred siblings
Coancestry (Θ)Out. Embedded ImageIn. Embedded Image
ProgramCov.Bias (×103)MSE (×104)Bias (×103)MSE (×104)
mapgd−102.2−11.62.5
VCFtools−6850−150230
KING−120170−4502000
mapgd10×−6.90.73−8.21.5
VCFtools10×−12.01.8−163.3
KING10×−214.7−5202700
mapgd30×−6.40.69−7.21.0
VCFtools30×−5.70.70−4.51.0
KING30×−3.10.29−5002500
Fraternity Embedded ImageOut. Embedded ImageIn. Embedded Image
ProgramCov.Bias (×103)MSE (×104)Bias (×103)MSE (×104)
mapgd−7.222−0.323
PLINK−207.17252
KING3701400230520
mapgd10×−1.74.3−1.45.8
PLINK10×112.3110120
KING10×58364001700
mapgd30×1.24.38.66.1
PLINK30×1.71.6120150
KING30×−3.51.73601300
Inbreeding Embedded ImageOut. Embedded ImageIn. Embedded Image
ProgramCov.Bias (×103)MSE (×104)Bias (×103)MSE (×104)
mapgdEmbedded Image−147.1−3318
VCFtoolsEmbedded Image99100−100110
PLINKEmbedded Image7254−150220
mapgdEmbedded Image−8.51.6−7.01.3
VCFtoolsEmbedded Image153.5−119.5
PLINKEmbedded Image122.4−7.41.2
mapgdEmbedded Image−9.01.9−7.61.6
VCFtoolsEmbedded Image−0.11.9−3.81.3
PLINKEmbedded Image−2.21.4−2.40.9
  • The values of all seven IBD coefficients are listed in Table S5 in File S1. Results are from 100 simulations on a 400-kbp, 400-cM genome containing Embedded Image SNPs. See Section S7 in File S1 for SNP filtering parameters. Out., outbred; in., inbred; cov. coverage. See figure S7 for diagram of outbred and inbred siblings.