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

Table 4 Deletion identification and classification of undescribed samples

Country	n	hrp2
Country	n	No Deletion	Deletion Classification (Partial/Complete)^a	ex1-/ex2 + ^b	ex1 + /ex2-^b	ex1-/ex2-^b
Cambodia	127	124	2/1	0	0	3
Brazil	20	16	2/2	0	1	3

Country	n	hrp3
Country	n	No Deletion	Deletion Classification (Partial/Complete)^a	ex1-/ex2 + ^b	ex1 + /ex2-^b	ex1-/ex2-^b
Cambodia	127	117	7/3	0	2	8
Brazil	20	5	1/14	0	1	14

^ahrp2/3 deletions assigned to isolates with > 25% CDS positions with zero coverage
^bExon absence (-) assigned to isolates if > 25% exon positions have zero coverage. ( +) signifies exon is present

ISSN: 1475-2875