Figure 2

Input and output formats for MalHaploFreq. (A) Input file format. Each line corresponds to a single blood sample. The first three indices are phenotypes at up to three codons where "0" indicates only wildtype is present, "2" mean only mutant are present,"1" means both wildtype and mutations are present. The fourth index is the multiplicity of infection (MOI). Assuming, for example, that dhfr is being analysed and that codons 1,2 and 3 represent positions 51, 59 and 108 respectively, then the first sample has only wildtype at position 51, only mutants at positions 59 and 108, and its MOI = 3. The second sample has only wildtype at position 51, has both wildtype and mutant and position 59, only mutant at position 108, and its MOI = 4. And so on throughout the input dataset. Missing data are indicated as '99' in the indices. (B) Output format. The indices represent codon genotypes, the first corresponding to codon 1, the second to codon 2 and the third to codon 3; within these brackets, "0" indicates wiltype and "1" indicates mutant. Assuming, as above, that dhfr is being analysed and that codons 1,2 and 3 represent positions 51, 59 and 108 respectively, then a haplotype mutant at only position 108 is encoded [0][0][1] and its estimated frequency is 3% with 95% CI of 1% to 8%. The 'double' mutant haplotype with mutations at positions 59 and 108 is encoded [0][1][1] and its estimated frequency is 86% with 95% CI of 79% to 92%. And so on.