TABLE 2.

Distribution of variable genes with nonsynonymous allelic variation by function^a

Functional group (no. in class per genome)	No. (%) of variable genesb		Nucleotide diversity (×10−5)b ,d
	All carriers	Without HGTc	All carriers	Without HGT	HGT only
Membrane associated (180)	25 (0.56)e	12 (0.32)e	5.1f	0.19f	27.5f
Metabolic functions (663)	31 (0.19)f	12 (0.07)f	2.0f	0.12f	11.9f
Regulation (325)	8 (0.1)f	3 (0.04)f	2.0f	0.08f	11.8f
DNA metabolism (104)	7 (0.27)f	6 (0.23)g	0.2f	0.16f	0.1f
Unknown function (855)	39 (0.18)f	13 (0.06)f	3.1f	0.22f	13.8f
Total (2,127)	110 (0.21)	46 (0.09)	2.3	0.15	12.0

^aA list of variable genes with nonsynonymous changes (i.e., with an altered amino acid sequence) was derived by analysis of alignments of derived amino acid sequence for each variable gene detected in the 25 pairs of persistent meningococcal isolates (Table 1). These genes were classified into one of five functional groups based on known functions or a homology-based analysis. Variable genes were also separated by occurrence in a carrier with or without high levels of HGT, with these classifications predicted to separate genes whose variation occurred by recombination from mutation.

^bThe denominator for calculating the percentage of variable genes was determined by multiplying the total number of genes in the class by the number of carriers.

^cNumbers of carriers in each group: all carriers, n = 25; without HGT, n = 21; HGT only, n = 4 (V54, V82, V128, and V222).

^dNucleotide diversity was calculated by using the average diversity for all genes to estimate the number of variants in a gene of 1,000 bp and then dividing this number by the total length of genes in a class (calculated by multiplying the number of genes by 1,000).

^eP, <0.001; chi-square test of observed versus expected.

^fNot significant by a chi-square test of observed versus expected for the number of variable genes or in one-way analysis of variance (ANOVA) for nucleotide diversity.

^gP, <0.01, chi-square test of observed versus expected.