Table 1.

Comparison of SNP-calls at 206 polymorphic positions in 206 MTBC genome sequence fastq files

	SNP in BWA mapping pipeline
	Yes		No		Total
	N	%	N	%	N	%
SNP in KvarQ	782	99.24	33	0.08	815	1.92
no SNP in KvarQ	6	0.76	41615	99.92	41621	98.08
Total	788	100	41648	100	42436	100