Table 1. Variant frequencies from targeted sequencing for Dam A.

							Dam A Targeted
							A-1		A-2		A-3
	Nucleotide			Amino acid			Plac	Fet	Plac	Fet	Plac	Fet
Gene	Pos	Ref	Alt	Pos	Ref	Alt	186x	189x	185x	147x	187x	194x
prM	693	A	G	196	T	A	19.7	25.3	35	10.5	11.8	6.3
M	798	T	C	231	S	P	12.6	29.6	34.5	16.1	12.4	7.7
Env	1087	A	G	327	D	G	4.8	14.5			10.4	2.1
NS1	3338	T	C	1077	T		20.3	13.8	13.2	8.7	15.5	<1
NS1	3535	T	C	1143	V	A	21.3	18	16.8	<1	21.5	10.1
NS2A	3650	C	T	1181	S		16.7	18.5	31.6	6.6
NS2A	3895	C	T	1263	A	V	27.9	23.8	20.6	<1	27.8	13.4
NS2A	4146	C	T	1347	L		20.3	23.1	26.9	15.2
NS2B	4319	G	A	1404	M	I	30.5	23	25.8	83.8	33.8	65.1
			T				8.4	15.3	5.7	1.1	7.9	3.2
NS3	5744	A	G	1879	T		12.1	7.5
NS3	6305	T	G	2066	D	E			10.5	1.9
NS3	6373	A	G	2089	K	R	22.2	17.3	24	7.7
NS5	8603	C	T	2832	A		22.5	19.9	28	85.5	25.2	74.7
quality score	≥90					# variable sites (10-90%):	11	11	11	5	8	4
	≤89					# dominant variant (≥90%):	0	0	0	0	0	0

x = average coverage per position of targeted sites