Figures and data
Summary of the datasets included in analysis
Ancestral populations included for global ancestry deconvolution
Genome-wide ancestral proportions of all individuals in the merged dataset. Ancestral proportions for each individual are plotted vertically with different colours representing different contributing ancestries
Local ancestry karyograms of three admixed individuals from the SAC population. Each admixed individual has unique local ancestry patterns generated by admixture among geographically distinct ancestral population groups
Log transformation of association signals obtained for KhoeSan ancestry whilst using the LAAA model on chromosome 6. The dashed red line represents the significant threshold for admixture mapping calculated with the software STEAM ( p-value = 2.5 x 10-6) and the black solid line represents the genome wide significant threshold ( p-value = 5 × 10 −8). The four different models are represented in black (global ancestry only - GAO), blue (local ancestry effect - LAO), orange (ancestry plus allelic effect - APA) and pink (local ancestry adjusted allelic effect - LAAA).
Regional plot indicating the nearest genes in the region of the lead variant (rs3117230) observed on chromosome 6. SNPs in linkage disequilibrium (LD) with the lead variant are coloured red/orange. The lead variant is indicated in purple. Functional protein-coding genes are coded in red and non-functional (pseudo-genes) are indicated in black.
Suggestive associations (p-value < 1e-5) for the LAAA analysis adjusting for KhoeSan local ancestry on chromosome 6
A schematic diagram the location of HLA-II genes associated with TB susceptibility. Genes in red were identified by the ITHGC. Genes in blue were identified by this study
Log transformation of association signals obtained for Bantu-speaking African ancestry whilst using the LAAA model on chromosome 20. The dashed red line represents the significant threshold for admixture mapping calculated with the software STEAM (p-value = 2.5 x 10-6) and the black solid line represents the genome-wide significant threshold (p-value = 5 × 10−8). The four different models are represented in black (global ancestry only - GAO), blue (local ancestry effect - LAO), orange (ancestry plus allelic effect - APA) and pink (local ancestry-adjusted allelic effect - LAAA).
QQ-plot of expected p-values and observed p-values for the association signals obtained for Bantu-speaking African ancestry located on chromosome 20
