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Table 2 Detectability of the minority clone in defined ratios of P. falciparum strains HB3 and 3D7

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

Ratios in mixtures cpmp csp Minimum Coverage HaplotypRc
HB3:3D7 3D7a
%
HB3a
%
PCR artefacts
%
Back-groundb
%
Coverage 3D7a
%
HB3a
%
PCR artefacts
%
Back-groundb
%
Coverage
1:1 34.6 57.4 0.48 7.53 40,768 34.7 50.5 5.79 9.01 9009 6
1:10 75.6 16.4 0.40 7.59 13,037 76.1 10.1 5.63 8.08 3341 30
1:50 88.8 3.15 0.06 7.95 4953 82.7 2.88 6.23 8.16 14,711 150
1:100 90.9 1.53 0.36 7.26 13,311 83.5 2.25 5.41 8.88 11,975 300
1:500 90.8 0.48 0.27 8.44 5649 84.0 0.46 4.76 10.8 3508 1500
1:1000 91.5 0.23 0.03 8.26 3039 85.7 0.22 5.09 9.02 1807 3000
1:1500 92.5 0.11 0.48 6.94 55,887 86.3 0.08d 5.71 7.91 23,619 4500
1:3000 92.5 0.094 0.38 7.00 7417 85.0 0.04d 5.87 9.10 2318 9000
  1. a Percent of reads that cluster with 3D7 and HB3 reference sequences
  2. b Singleton reads and reads that failed to cluster with 3D7 or HB3 haplotypes
  3. c Theoretical minimum required coverage needed to detect minority clone by software HaplotypR with default cut-off values
  4. d Haplotypes considered as noise by software HaplotypR (default cut-off: ≥3 reads per haplotype and a minority clone detection limit of 1:1000)