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Table 3 Deletion identification and classification of previously genotyped samples

From: Gene Coverage Count and Classification (GC3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum

Country

n

hrp2

No Deletion

GC3 Deletion Classification (Partial/Complete)a

ex1-/ex2 + b

ex1 + /ex2-b

ex1-/ex2-b

Previous Genotype (Deletion/Total)c

Kenya

59

58

0/1

0

0

1

2/27

Peru

11

10

1/0

1

0

0

0/12

Country

n

hrp3

No Deletion

GC3Deletion Classification (Partial/Complete)a

ex1-/ex2 + b

ex1 + /ex2-b

ex1-/ex2-b

Previous Genotype (Deletion/Total)c

Kenya

59

58

1/0

0

0

1

1/27

Peru

11

9

2/0

0

1

1

2/12

  1. ahrp2/3 deletions assigned to isolates with > 25% CDS positions with zero coverage
  2. bExon absence (-) assigned to isolates if > 25% exon positions have zero coverage. ( +) signifies exon is present
  3. cPrevious hrp2/3 deletion genotype results from Sepúlveda and colleagues. Deletions called for samples with > 75% of coding region with ≤ 2X coverage [19]