Table 2.

Summary of M. tuberculosis data sets used for joint genotyping. “Genome inside sites” is the total length of all reference alleles across all sites after clustering. It is reported as the total number of base pairs, and in parentheses as a percentage of the 4.4Mbp H37Rv reference genome. SNP sites is the number of sites where all alleles have length 1

Data set	Number of samples	Unique variants	Excluded variants	Sites after clustering	Genome inside sites (bp(%))	Total alleles	SNP sites
Walker 2013	385	31,548	231	30,621	41,437 (1%)	62,690	27,639
Mykrobe	13,411	699,484	6,259	593,584	756,003 (17%)	1,414,723	552,543
CRyPTIC	15,215	718,863	6,576	611,269	778,949 (18%)	1,469,100	568,224