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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