Analysis of the secondary African genomic data to identify allele frequencies in genetic determinants associated with varying outcomes of COVID-19 in other population groups

This dataset listed here contains supplementary data supporting Chapter 3, 4, 5 and 6 of the thesis "Analysis of variants in host genes associated with COVID-19 outcomes in the African population." The data includes raw genotype calls, processed summary tables, and supporting analyses to enable understanding of the thesis chapters.Appendix B includes the following supplementary files:Supplementary_File_1 (list of COVID-19 genetic articles)Supplementary_File_2_T1/T2 (list of COVID-19 associated variants and genes identified in LD)Pipeline_Script (pipeline code used to analyse sequencing data)Gene_Transcripts (transcript identifiers used for each gene)Gene_Locations (the location and gene length information used)Appendix C includes the following supplementary files:Supplementary data has been published under the DOI https://doi.org/10.1038/s41431-022-01089-8 and includes-Appendix_C_Supplementary Data AAppendix_C_Supplementary Data BAppendix_C_Supplementary Data CAppendix_C_Supplementary Notes and Supplementary Figure 1Appendix_D includes the following supplementary files:Appendix_D_Supplementary_Data_A- (List of previously published COVID-19 variants assessed in the AFR population and the AF’s of each variant in the AFR, EUR, EAS, SAS and AMR population groups).Appendix_D_Supplementary_Data_B- (Raw frequency data for each variant, including p-values and odds ratios).Appendix E includes the following supplementary files:Appendix_E_Supplementary_Data_A- (Includes 5 tables)T1: Sample list for the GnomAD dataT2: Gene Function/ category information for 153 COVID-19 associated genesT3: 39 biologically plausible candidate genes and total variants identified across all populations analysed using the pipelineT4: High priority list of 20 candidate genes analysed in chapter 6T5: AF and raw data for the 43 common AFR variantsAppendix_E_Supplementary_Data_B (Functional prediction data for variants in genes ACE2, IL10RB and TMPRSS2)Appendix_E_Supplementary_Data_C (Functional prediction data for variants in genes TYK2, DPP9, OAS1-3)Appendix_E_Supplementary_Data_D (Functional prediction data for variants in genes MUC5B, ELF5, SFTPD and IFNA10)Appendix_E_Supplementary_Data_E (Functional prediction data for variants in genes FOXP4, IRF1 and PLSCR1)Appendix_E_Supplementary_Data_F (Functional prediction data for variants in genes LZTFL1 and JAK1)