Table 1.

Summary of SNP Distribution and SNP Predictions among Functional Categories for the Lineage-Specific SNPs

	Lineage SNPs
Functional Categorya	Nonsynon	Synon	Nonsynon/Synon	χ2 P Value	Predicted Functional SNPsb
	1,543	840	1.8		368
Information pathways	96	73	1.3	0.11	12
Lipid metabolism	168	99	1.7	0.63	66
Intermediary metabolism and respiration	394	237	1.7	0.40	88
Cell wall and cell processes	377	197	1.9	0.63	91
Conserved hypotheticals	343	174	2.0	0.63	63
Virulence, detoxification, adaptation	63	29	2.2	0.63	17
Regulatory proteins	102	31	3.3	0.03	31
Intergenic	382		N/A	N/A	N/A

Note.—A 3-fold overrepresentation of nonsynonymous (nonsynon) to synonymous (synon) SNPs was found within the category of transcriptional regulators (χ², P = 0.03).

^aCategories are based on Tuberculist annotations.

^bFunctional SNPs predicted using SIFT (SIFT score ≤ 0.05).