Table 2

MLST of completely sequenced bacterial isolates using short sequence reads

Sequencing platformSpeciesNo. of isolatesMLST schemeProportion of loci with:Avg N50Log avg N50
Minor mismatchesMajor mismatches
Illumina
    Paired-end readsB. animalis5Bifidobacterium0.0000.02933,1134.52
C. jejuni53Campylobacter0.0050.000131,5715.12
E. coli15E. coli scheme 10.0100.000195,8225.29
E. coli15E. coli scheme 20.0750.000196,4635.29
K. pneumoniae4K. pneumoniae0.0000.000207,1675.32
L. lactis34L. lactis0.5640.03944,5254.65
S. aureus83S. aureus0.0170.009196,7365.29
S. enterica50S. enterica0.0000.009249,5015.40
S. thermophilus13S. thermophilus0.0900.00047,6864.68
    Single readsE. coli6E. coli scheme 10.0000.00046,4794.67
B. animalis2Bifidobacterium0.0000.07124,9794.40
B. longum2Bifidobacterium0.0000.00022,5484.35
L. lactis7L. lactis0.2380.11914,1144.15
P. aeruginosa81P. aeruginosa0.0190.1259,3803.97
S. thermophilus9S. thermophilus0.0000.00028,8234.46
Roche 454E. coli3E. coli scheme 10.0000.00092,1314.96
P. aeruginosa2P. aeruginosa0.0000.00060,4774.78
Ion TorrentE. coli2E. coli scheme 10.0000.50013,7794.14
SOLiDE. coli1E. coli scheme 10.2860.000165,8355.22