Version 2 of data for 'Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa'.

Dataset 1: Information on the 276 SNPs genotyped in 177 genes in P. falciparum parasite populations from The Gambia, Kilifi and Rachuonyo South. The columns contain the following information: study_location, site of sample collection; sample_id, unique sample identifier; gene_symbol, gene name (if available); chr_valid, chromosome; coord_valid= base position of SNP on chromosome; sequence_code, SNP name; assay_code, name of assay; rsnumber, unique SNP identifier in dbSNP; reference_allele, 3D7 reference allele, alternative_allele, alternative allele; single letter code, IUPAC code for SNPs; result, genotype call after processing; allele1, IUPAC code for allele 1; allele2, IUPAC code for allele 2; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass) or lack of a valid genotype (fail). Geospatial data for homestead location is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee, using the email address mmunene@uat/newsite.

Dataset 2: Sequenom assay design information. Data includes the locus and IPLEX specific primers used in the sequenom reaction to amplify and type the SNPs of interest. Gene product, gene product name; Gene_symbol, gene name; Chromosome, chromosome location of gene; SNP position on chromosome, SNP site; reference allele, 3D7 reference allele; alternative allele, alternative allele; sequence, 3D7 reference sequence spanning the SNP site; first_pcrp, first PCR primer sequence; second_pcrp, second PCR primer sequence; extension_primer, IPLEX extension primer sequence; extension1_call, IPLEX primer with extended SNP; extension1_mass, Mass of the extended IPLEX primer; extension1_sequence, sequence of extended IPLEX primer; extension2_call= IPLEX primer with alternative extended allele; extension2_mass, Mass of the extended IPLEX primer with alternative allele; extension2_sequence, sequence of extended IPLEX primer with alternative allele.

Dataset 3: SNP, distance and time differences between P. falciparum parasite pairs in The Gambia population. Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of snp differences between parasite pairs; km_distance represents geographical distance, in kilometres, between parasite pairs; time_diff represents the temporal distance, in days, between parasite pairs.

Dataset 4: SNP, distance and time differences between P. falciparum parasite pairs in the Kilifi population. Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of snp differences between parasite pairs; km_distance represents geographical distance, in kilometres, between parasite pairs; time_diff represents the temporal distance, in days, between parasite pairs.

Dataset 5: SNP and distance differences between P. falciparum parasite pairs in the Rachuonyo South population. Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of snp differences between parasite pairs; km_distance represents geographical distance, in kilometres, between parasite pairs.