Table 4.

Concordance of haplotype calls in replicates of 37 field samples

	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

Bold rows indicate haplotypes that did pass cut-off criteria in both replicates

^a Default cut-off criteria to accepted haplotype ≥3 reads and a minority clone detection limit of 1:1000

^b Owing to default cut-off for haplotype call

^c Second replicate had too low coverage to detect ≥3 reads

^d Potential false haplotype calls as only one replicate passed cut-off criteria

^e In 2 instances second replicate had too low coverage to detect minority clone