Table 2.

Samples selected for WGS

Sample	Parasite count	Leukocyte count	Parasitaemia (paras./μl)	Parasitaemia (%)	Malaria (%)	Human (%)	Other (%)	Average read depth	Coverage
1	98	200	3920	0.1	46.1	35.2	18.7	16×	87.5
2	214	200	8560	0.2	67.1	13.7	19.2	15×	88.4
3	420	200	16,800	0.4	62.2	6.4	31.4	41×	95.3
4	500	102	39,216	1.0	81.7	3.5	14.8	67×	97.8
5	500	83	48,193	1.2	48.1	15.6	36.3	99×	98.9

Parasitaemia is given as parasites/µl (as described in Table 1, and in “Methods”) as well as in percentage, which is calculated according to an assumed erythrocyte count of 4000,000 erythrocytes per µl whole blood. Sequencing reads were mapped to a variety of databases, including a human database and a malaria database, using MGmapper (see “Methods”) [18]. The percentage of raw reads mapping to human, malaria and other databases are listed, as well as the average read depth of the sample and coverage as compared to the 3d7 reference genome