Table 1.
Sources of the high‐coverage whole genome sequence data sets used in the study
| Populations | Project/Institution | n |
|---|---|---|
| H3Africa Consortium data | ||
| Fon from Benin (FNB) | H3Africa Baylor; University of Montréal | 50 |
| Berom of Nigeria (BRN) | H3Africa Baylor; Institute of Human Virology | 49 |
| Cameroon (CAM) | H3Africa Baylor; University of Dschang | 26 |
| Ghana (GHA) | H3Africa Baylor; AWI‐Gen | 26 |
| Burkina Faso (BFA) | H3Africa Baylor; AWI‐Gen | 33 |
| South Africa | AWI‐Gen | 100 |
| Botswana (BOT) | H3Africa Baylor; CAfGEN | 47 |
| Bantu‐speakers from Zambia (BSZ) | H3Africa Baylor; University of Zambia | 41 |
| Data from other Africa‐based projects | ||
| South Africa | SAHGP | 15 |
| South Africa | CBRL (NICD; Wits University) | 40 |
| African genomes in public repositories | ||
| Botswana/Namibia | SGDP | 3 |
| Namibia | SGDPa | 3 |
| DRC | SGDPb | 4 |
| Gambia | SGDP | 2 |
| Kenya | SGDPc | 5 |
| Nigeria | SGDP | 4 |
| Senegal | SGDP | 3 |
| South Africa | SGDPa | 3 |
| South Sudan | SGDPc | 3 |
| Luhya in Webuye, Kenya (LWK) | 1000 Genomes Project | 99 |
| Esan in Nigeria (ESN) | 1000 Genomes Project | 99 |
| Yoruba in Ibadan (YRI) | 1000 Genomes Project | 108 |
| Mende in Sierra Leone (MSL) | 1000 Genomes Project | 85 |
| Gambian in Western Division, Mandinka (GWD) | 1000 Genomes Project | 113 |
| Public data sets with genomes from other global superpopulations (for comparative analysis) | ||
| African Caribbean in Barbados (ACB) | 1000 Genomes Project | 96 |
| People with African Ancestry in Southwest United States (ASW) | 1000 Genomes Project | 61 |
| European (EUR) | 1000 Genomes Project | 503 |
| Admixed American (AMR) | 1000 Genomes Project | 347 |
| South Asian (SAS) | 1000 Genomes Project | 489 |
| East Asian (EAS) | 1000 Genomes Project | 504 |
The genomes of all the study participants were sequenced to an average read depth of ∼30× by the respective projects indicated in the table.
AWI‐Gen, Africa Wits‐INDEPTH partnership for Genomics studies; CAfGen, The Collaborative African Genomics Network; CBRL, Cell Biology Research Laboratory; NICD, National Institute for Communicable Diseases; SAHGP, Southern African Human Genome Programme; SGDP, Simons Genome Diversity Project.
The majority of the continental African participants referred to in this table are from the Niger‐Congo language family, except the following:
Khoe and San hunter‐gatherers.
Pygmy hunter‐gatherers.
Nilo‐Saharan (n = 2 for the Kenyan SGDP participants).