Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections

Table 1 Diversity of markers cpmp and csp based on 3′411 genomes of the MalariaGen dataset

Marker	H_e ^a	No. of SNPs	Fragment size^b	No. of Haplotypes
cpmp	0.930^c	20^c	383^c	82 of 980^c,d
csp	0.857	40	287	77 of 1323^d

^aExpected heterozygosity
^bFragment size without primer sequence
^cTrimming of reads in the here presented experiments led to a reduction of variation (Characteristics for a shorter cpmp fragment size of 310 bp: He = 0.913, SNPs = 14 and number of haplotypes = 47)
^dFrom 3411 genomes only genomes with non-ambiguous SNP calls in selected region were used

ISSN: 1471-2164