Table 1. Tagging status of the 53 rMLST loci used in analysis.

Parameter	IMG genome status			S. pneumoniae velvet assemblies
	Draft	Complete	Total
Strains uploaded	920	982	1902	28
Mean contigs per strain	215.5	1.7	105.1	354.6
Strains with all rMLST loci tagged	499	674	1173	28
Average complete rMLST genes per strain*	48.94 (53)	52.59 (53)	50.82 (53)	52.6 (53)
Average partial rMLST genes per strain*	1.077 (0)	0.003 (0)	0.523 (0)	0.39 (0)
Average missing rMLST genes per strain*	2.990 (0)	0.404 (0)	1.655 (0)	0.00 (0)
Average internal stop codons per strain*	0.702 (0)	0.329 (0)	0.509 (0)	1.00 (1)

^*Averages: main values are mean; modal values are in parentheses.