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

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

Marker He a No. of SNPs Fragment sizeb No. of Haplotypes
cpmp 0.930c 20c 383c 82 of 980c,d
csp 0.857 40 287 77 of 1323d
  1. aExpected heterozygosity
  2. bFragment size without primer sequence
  3. 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)
  4. dFrom 3411 genomes only genomes with non-ambiguous SNP calls in selected region were used
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BMC Genomics

ISSN: 1471-2164

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