Selections, frameshift mutations, and copy number variation detected on the surf 4.1 gene in the western Kenyan Plasmodium falciparum population

Table 1 Nucleotide diversity of Plasmodium falciparum surf _4.1 in western Kenyan isolates (n = 24)

Region (position)	Number of sites (base)	Indels	k	Nd	N	Sd	S	π	d _N	d _S	d _N/d _S	p
Region (position)	Number of sites (base)	Indels	(SE)	(SE)	(SE)	(SE)	(SE)	(SE)	(SE)	(SE)	d _N/d _S	(d _N > d _S)
Extracellular	2286	9	104.64	87.22	1791.60	17.43	488.40	0.048	0.051	0.037	1.38	0.004
(4–2289)			(5.50)	(6.03)	(8.40)	(2.25)	(8.40)	(0.003)	(0.003)	(0.005)
Nter	147	0	0.24	0.24	118.30	0.00	28.70	0.002	0.002	0.000	∞	ns*
(4–150)			(0.19)	(0.17)	(2.01)	(0.00)	(2.10)	(0.001)	(0.002)	(0.000)
CRD	435	0	2.99	1.52	351.61	1.47	80.39	0.007	0.004	0.019	0.21	ns*
(151–585)			(1.11)	(0.70)	(3.68)	(0.79)	(3.64)	(0.003)	(0.002)	(0.011)
Var1	918	3	20.23	17.86	721.42	2.37	196.58	0.023	0.026	0.012	2.17	ns*
(586–1506)			(2.15)	(2.16)	(5.52)	(0.64)	(5.57)	(0.002)	(0.003)	(0.003)
Var2	783	6	81.19	67.60	600.28	13.59	182.72	0.115	0.126	0.080	1.58	0.0003
(1507–2289)			(4.73)	(4.62)	(4.74)	(1.97)	(4.57)	(0.007)	(0.009)	(0.011)

Extracellular, extracellular region; Nter, N-terminal segment; CRD, cysteine-rich domain; Var1, variable region 1; Var2, variable region 2; sites, sites nucleotide analyzed; indels, insertion/deletion polymorphism; k, the average number of nucleotide differences; N and S, average numbers of nonsynonymous and synonymous sites; π, pairwise nucleotide diversity (Jukes-Cantor model); d _N, mean number of nonsynonymous substitutions per nonsynonymous site; d _S, mean number of synonymous substitutions per synonymous site; SE, standard error computed using the Nei-Gojobori method with the Jukes-Cantor correction. SE was estimated using the bootstrap method with 500 replication
The numbers of synonymous (Sd) and nonsynonymous (Nd) differences were calculated by the Nei-Gojobori method. p value indicates the statistical difference between d _N and d _S, tested using one-tail Z-test with 500 bootstrap pseudo samples implemented in MEGA. ns indicates not significant by two-tailed Fisher’s exact tests (*). Number is after 3D7 line sequence

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