Table 1. Specificity and sensitivity of the capture-based parasite DNA enrichment approach.

Isolate	Pre-enrichment Theileria gDNA (%)a	Total reads generatedb	Total reads aligned	Mean coveragec	Specificity (%)d	Sensitivity (%)e
BV115	1.94	12,174,316	11,952,650	146X	98.03	99.80
Marikebuni 3292	3.05	7,204,556	6,740,297	202X	96.47	97.70
Uganda 3645	0.92	5,687,838	5,313,295	157X	97.52	98.34
Buffalo_3081	1.72	6,080,972	5,446,541	160X	96.40	97.59

^a Proportion of the original DNA sample that is composed of T. parva DNA, as measured by qPCR [36].

^b Read length for BV115 was 101 bp and 250 bp for the other three strains.

^c Estimation: (Total_reads_aligned*Mean_read_length)/genome_size. The genome size used was the sum of the nuclear and apicoplast reference genomes targeted.

^d Percent reads generated that mapped to T. parva reference genome.

^e Percent of the T. parva reference genome to which reads map.