Table 2. Comparison of SNP frequency and distribution between P. vivax and P. falciparum.

	P. vivax			P. falciparum
Polymorphism	No. bp screened	No. of SNPs	π (×10-4), mean±SE	No. bp screened	No. of SNPs	π (×10-4), mean±SE
Total SNPs	100,388*	191	8.7±0.9	218,152	238	4.9±1.3
Noncoding	50,621	125	11.2±1.3	16,083	31	9.4±0.9
Intron	4,719	5	5.8±0.5	16,083	31	9.4±0.9
Intergenic	45,902	120	11.7±1.3	—	—	—
Coding	49,767	66	6.3±0.5	202,069	207	4.4±0.6
Synonymous	10,758	24	10.6±2.8	38,480	62	6.8±1.0
Nonsynonymous	38,893	42	5.1±1.7	163,498	145	3.9±0.6
Repeats	100,388	44†		218,152	165

The P. falciparum polymorphisms were identified from noncontiguous DNA sequences where most of the noncoding sequences analyzed were introns (14). Both data sets were derived from five Plasmodium isolates. Nucleotide counts were based on the P. vivax YAC 1H14 reference sequence. Synonymous and nonsynonymous sites were calculated by using DNASP after excluding alignment gaps. Gene models are shown according to published predictions (9,47). π was estimated as described in Methods

^*Repeat regions within the csp genes from both parasites have been excluded from all calculations

^†Number of polymorphic repeats, including simple sequence repeats and TRs