Skip to main content

Table 1 Nucleotide diversity of Plasmodium falciparum surf 4.1 in western Kenyan isolates (n = 24)

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

Region (position) Number of sites (base) Indels k Nd N Sd S π d N d S d N/d S p
(SE) (SE) (SE) (SE) (SE) (SE) (SE) (SE) (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)   
  1. 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
  2. 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