Distribution of single nucleotide polymorphisms assayed and resulting molecular bar codes for sequenced parasites. Twenty-four SNPs with an average minor allele frequency of at least 35% that were unlinked and assayable by TaqMan technology were selected from SNPs identified across the P. falciparum genome from sequencing efforts. The positions of the SNPs on the 14 chromosomes of P. falciparum are shown in A, with the sequence of the major and minor allele for each of the SNPs that comprise the molecular bar code shown in B. The position numbers in B (1 to 24) correspond to the positions in A, beginning with chromosome 1 through chromosome 14 and on each chromosome starting with the lowest coordinate number  and proceeding to the highest coordinate number on that chromosome (See Additional File 10). The major allele is indicated by a gray box and the minor allele by a white box. The yellow box (with an X) indicates no amplification. In all cases the TaqMan assay results matched sequence information.