Single nucleotide polymorphism (SNP) data
SNP barcoding data
SNP barcode data from the sanger 100 SNP Plasmodium falciparum barcode (Chang et al. 2019).
sanger101_snp_barcode_withGenes.bed
Field Samples
The barcode was subsetted from the above WGS data to just the sanger barcode for the Vietnam and DRC data. The results file can be found within directory snp_barcode/sangerBarcode_SNP_INDEL_Pf3D7_ALL_v3.combined.filtered.vqslod6.biallelic_snp.Vietnam.vcf.gz, snp_barcode/sangerBarcode_SNP_INDEL_Pf3D7_ALL_v3.combined.filtered.vqslod6.biallelic_snp.DRCongo.vcf.gz
Lab Isolates
The barcode was also explicitly called with several monoclonal lab isolates and then lab created mixtures of these isolates. Data can be found snp_barcode/controls_sanger100.vcf.gz with meta data with what mixtures are what found snp_barcode/allControlMixtures.tab.txt and snp_barcode/allControlSampNameToMixName.tab.txt
Simulated
The barcode was also simulated for 100 samples (50 Bangladesh and 50 Ghana). Data can be found snp_barcode/SpotMalariapfPanel_simData_sanger100.vcf.gz. The simulations were created by simulating super infections by sampling the barcode from each of these countries and selecting COIs based on the COIs observed for each country. To use data without indels, the data can be found snp_barcode/SpotMalariapfPanel_simData_snponly_sanger100.vcf.gz.