Supplementary Table 4. Comparison of Ancestry methods

We ran HAPMIX and LAMP-LD with 1000G phase 3 haplotypes. The European source panel consisted of 503 samples from British From England and Scotland [GBR], Toscani in Italia [TSI], Iberian Populations in Spain [IBS], Finnish in Finland [FIN] , and CEPH (U.S. Utah residents with ancestry from northern and western Europe) [CEU]. The African source panel consisted of 504 samples from Esan in Nigeria [ESN], Gambian in Western Division – Mandinka [GWD], Luhya in Webuye, Kenya [LWK], Mende in Sierra Leone [MSL] and Yoruba in Ibadan, Nigeria [YRI]. We retrieved phased alleles for 1,343,587 markers. We also ran LAMP-LD with only CEU and YRI populations. We applied the same filtering criteria to all the three analysis as described in the paper and the compared them.