Table 2.

MLST of completely sequenced bacterial isolates using short sequence reads

Sequencing platform	Species	No. of isolates	MLST scheme	Proportion of loci with:		Avg N50	Log avg N50
				Minor mismatches	Major mismatches
Illumina
Paired-end reads	B.animalis	5	Bifidobacterium	0.000	0.029	33,113	4.52
	C. jejuni	53	Campylobacter	0.005	0.000	131,571	5.12
	E. coli	15	E. coli scheme 1	0.010	0.000	195,822	5.29
	E. coli	15	E. coli scheme 2	0.075	0.000	196,463	5.29
	K. pneumoniae	4	K. pneumoniae	0.000	0.000	207,167	5.32
	L. lactis	34	L. lactis	0.564	0.039	44,525	4.65
	S. aureus	83	S. aureus	0.017	0.009	196,736	5.29
	S. enterica	50	S. enterica	0.000	0.009	249,501	5.40
	S. thermophilus	13	S. thermophilus	0.090	0.000	47,686	4.68
Single reads	E. coli	6	E. coli scheme 1	0.000	0.000	46,479	4.67
	B. animalis	2	Bifidobacterium	0.000	0.071	24,979	4.40
	B.longum	2	Bifidobacterium	0.000	0.000	22,548	4.35
	L. lactis	7	L. lactis	0.238	0.119	14,114	4.15
	P. aeruginosa	81	P. aeruginosa	0.019	0.125	9,380	3.97
	S. thermophilus	9	S. thermophilus	0.000	0.000	28,823	4.46
Roche 454	E. coli	3	E. coli scheme 1	0.000	0.000	92,131	4.96
	P. aeruginosa	2	P. aeruginosa	0.000	0.000	60,477	4.78
Ion Torrent	E. coli	2	E. coli scheme 1	0.000	0.500	13,779	4.14
SOLiD	E. coli	1	E. coli scheme 1	0.286	0.000	165,835	5.22