Table 2. Genotype call comparison for selected loci.

Chr stands for chromosome, locus for genomic coordinates, A1 for allele 1, A2 for allele 2, angle for arctangent value from two variable (=atan2(A1,A2)), and GT for genotype calls based on angle value. If arctangent value is less than 0.25, it is considered as A1/A1 homozygote. If value is higher than 1.25, genotypes are called as A2/A2. Otherwise, genotoypes are called as heterozygote (A1/A2).

			Original DNA				WGA
Sample	Chr	Locus	A1 depth	A2 depth	ANGLE	GT	A1 depth	A2 depth	ANGLE	GT	Same?
A. gambiae 1	Mt	3164	189	0	0	A1/A1	9	3	0.3218	A1/A1	yes
A. gambiae 1	Mt	3211	168	0	0	A1/A1	17	4	0.2311	A1/A1	yes
A. gambiae 1	2R	19625228	2	0	0	A1/A1	56	0	0	A1/A1	yes
A. gambiae 1	2R	19625240	3	0	0	A1/A1	1	59	1.5538	A2/A2	NO
A. gambiae 1	2R	19625389	0	0	-	no call	0	73	1.5708	A2/A2	NO
A. gambiae 1	2R	19650738	2	0	0	A1/A1	1	10	1.47118	A2/A2	NO
A. gambiae 1	2R	19728934	1	1	0.7854	A1/A2	0	7	1.5708	A2/A2	NO
A. gambiae 1	2R	19738843	3	0	0	A1/A1	3	10	1.27938	A2/A2	NO
A. gambiae 1	X	23752288	2	1	0.4636	A1/A2	2	2	0.7854	A1/A2	yes
A. gambiae 1	X	23756047	3	0	0	A1/A1	2	1	0.4636	A1/A2	NO
A. gambiae 1	X	23779162	0	4	1.5708	A2/A2	0	0	-	no call	NO
A. gambiae 2	Mt	8276	714	1	0.0014	A1/A1	7	8	0.8520	A1/A2	NO
A. gambiae 2	Mt	8840	3	774	1.5669	A2/A2	0	6	1.5708	A2/A2	yes
A. gambiae 2	Mt	8927	22	817	1.5439	A2/A2	4	6	0.9828	A1/A2	NO
A. gambiae 2	Mt	9098	559	0	0	A1/A1	8	2	0.2450	A1/A1	yes
A. gambiae 2	2R	19850861	14	5	0.3430	A1/A2	4	2	0.4636	A1/A2	yes
A. gambiae 2	2R	19850867	17	1	0.0588	A1/A1	5	0	0	A1/A1	yes
A. gambiae 2	2R	19851283	9	8	0.7266	A1/A2	4	2	0.4636	A1/A2	yes
A. gambiae 2	X	22010492	6	3	0.4636	A1/A2	8	1	0.1244	A1/A1	NO
A. gambiae 2	X	22011555	9	6	0.5880	A1/A2	4	63	1.5074	A2/A2	NO
A. gambiae 2	X	22013224	10	3	0.2915	A1/A1	60	1	0.0167	A1/A1	yes