Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer

Table 2 Efficacy of SNP calling using the consensus sequence or H37Rv as the reference genome by comparing the number of SNPs detected

i) individual strains
Species	Strain	vs H37Rv	vs consensus sequence
M. tuberculosis	CCDC5079	632	198*
	CCDC5180	378	70*
	CDC1551	543	41*
	CTRI-2	140	15*
	Erdman	570	104*
	F11	343	129*
	H37Ra	44	38*
	H37Rv		12
	KZN605	16	9
	KZN1435	12	2
	KZN4207	26	0
	RGTB327	1242	127*
	RGTB423	2410	145*
M. bovis BCG	Mexico	13	0
	Moreau RDJ	136	22*
	Pasteur	20	0
	Tokyo 172	56	76*
M. africanum	GMO41182	876	152*
M. canettii	CIPT 140010059	24425*	560
Total SNP found in only one strain		31882	1700
	ii) group comparison
	four BCG strains	1040	52*
	three KZN strains	121	15
	All SNP at least found in one strain	37589	3429

Based on SNP calls using MUMmer [58], the number of SNPs called uniquely in individual strains, and in groups of BCG and KZN strains, was determined. *The number of SNPs detected using the H37Rv and consensus sequences as reference were compared for each strain (i) or group of strains (ii) using Fisher's exact test, with significant differences indicated with asterisks (p < 0.0001).

ISSN: 1471-2164