Performance Testing on Real Population Data:
1000G phase 3 from data was used to test ROHMM ’s inference capabilities on real population data. ROHMM was run with parameters used to test the simulated data performance. Inferred homozygosity within subpopulations were compared against the inbreeding coefficient calculated via the method of moments estimator usingPLINK het and in-house script. Meta analysis of inferences also included comparison of different ROH categories among different sub and super populations as indicated by others (Keller, Visscher, & Goddard, 2011; Magi et al., 2014; Narasimhan et al., 2016; Pemberton et al., 2012). Inferred ROHs were also compared against the heterozygosity measure as mentioned by Samuels and colleagues (Samuels et al., 2016).