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Table 4 Concordance of haplotype calls in replicates of 37 field samples

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

  cpmp csp Passed cut-offa
Haplotype frequency within sample ≥ 1%
present in both replicates 87 57 yes
 present in single replicate only 0 0 no
Haplotype frequency within sample < 1%
present in both replicates at ≥ 3 reads b 2 0 yes
 present in both replicates one ≥ 3 readsb and one < 3 readsb 1c 0 yes/nod
 present in single replicate at ≥ 3 readsb 17e 2 yes/nod
 present in both replicates at < 3 readsb 1 0 no
 present in single replicate at < 3 readsb 10 5 no
  1. Bold rows indicate haplotypes that did pass cut-off criteria in both replicates
  2. a Default cut-off criteria to accepted haplotype ≥3 reads and a minority clone detection limit of 1:1000
  3. b Owing to default cut-off for haplotype call
  4. c Second replicate had too low coverage to detect ≥3 reads
  5. d Potential false haplotype calls as only one replicate passed cut-off criteria
  6. e In 2 instances second replicate had too low coverage to detect minority clone