Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis

Table 2 Significant genes identified by the de novo genome assembly analysis

	Discovery dataset (n = 108)			Validation dataset (n = 214)
	Strains with CDS present (N)			Strains with CDS present (N)
Coding sequence	TBM (n = 54)	PTB (n = 54)	P-value	TBM (n = 52)	PTB (n = 162)	P-value^
Bifunctional NAD(P)H-hydrate repair enzyme Nnr (Rv3433c)	36	47	0.011	34	144	0.002
TMAO/DMSO reductase	46	53	0.016	49	152	0.592
Antitoxin/MT2731	33	44	0.017	37	130	0.206
NPCBM-associated, NEW3 domain of alpha-galactosidase	15	6	0.022	14	19	0.063
Oxidoreductase molybdopterin binding domain protein	11	3	0.028	7	13	0.197
N-acetylmannosamine kinase (nanK)	44	51	0.036	44	157	0.001

NOTE. P-values are based on permutation analysis; bold p-values indicate validated significant enrichment
^ P-value thresholds in the validation set were Bonferroni-corrected for multiple testing by dividing them by the number of top hits in the discovery set: p < 0.05/6

ISSN: 1471-2164