Table 2 Inference and phasing error for the 250 Pseudo Embedded Image lines based on the KE DH-lines for chromosome 10. * BEAGLE crashed for this dataset when using phase-segment > 10, phase-states < 100 or phase-states > 10,000
Parameterdefaultrange testedbest inferencebest phasingoverall impact
BEAGLE 5.1default (0.0239%)default (2,540)
ne1,000,0001 - 1,000,00030 (0.0168%)10 (3,206)Figure S26
err0.000150.05 - 0.000010.0005 (0.0229%)0.05 (2,556)Figure S28
window4010 - 1,000200 (0.0179%)200 (2,581)Figure S30
burnin62 - 2525 (0.0229%)2 (2,555)Figure S32
iterations122 - 40default40 (2,638)Figure S34
phase-states280100* - 10,000*10,000 (0.0168%)5,000 (2,675)Figure S37
imp-states, imp-segment, cluster, imp-step, imp-nsteps1,600, 6, 0.005, 0.1, 7only impacts UM imputation
BEAGLE 5.0default (0.0138%)default (2,716)
ne1,000,0001 - 1,000,0001 (0.0111%)30,000 (3,136)Figure S25
err0.00010.05 - 0.000010.005 (0.133%)0.001 (2,747)Figure S27
window4010 - 200100 (0.0139%)200 (2,737)Figure S29
burnin62 - 252 (0.0136%)2 (2,748)Figure S31
iterations122 - 4020 (0.0135%)40 (2,760)Figure S33
phase-segment41 - 10*10 (0.132%)10 (2,758)Figure S35
phase-states280100* - 10,000*10,000 (0.0130%)5,000 (2,815)Figure S36
imp-states, imp-segment, cluster1,600, 6, 0.005only impacts UM imputation
BEAGLE 4.1default (0.0345%)default (2,617)
niterations50 - 2525 (0.0249%)25 (3,392)Figure S38
modelscale0.80.5 - 51 (0.0198%)1 (3,223)Figure S39
ne1,000,0001 - 1,000,00030 (0.0325%)30,000 (2,999)Figure S40
BEAGLE 4.0default (0.119%)default (1,240)
buildwindow1,2001 - 5,00050 (0.0316%)5,000 (1,618)Figure S41
singlescale0.80.5 - 51.0 (0.0626%)1.25 (1,955)Figure S42
nsamples41 - 5050 (0.0780%)50 (2,308)Figure S43
burnin-its52 - 5050 (0.108%)50 (1,599)Figure S44
phase-its52 - 5050 (0.0944%)50 (2,320)Figure S45
impute-its52 - 50only impacts UM imputation