Table 1.
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).