Table 1 Overview of data collected and sequence quality. SA: Source attribution. BN: BioNumerics.

From: Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

Dataset Years included Total sequences collected for the study Poor quality Excluded for other reasons Included in SA study
n total = 1781
n humans = 943
n animal = 804
n environment = 34
FoodQC BN QC FoodQC + BN QC n total = 1259
(n animal = 753, n human = 479, n environment = 29)
DK food 2013, 2014 211 1 0 0 0 210
DK human 2013, 2014 181 0 40 0 0 141
UK Food 2014, 2015, 2016 329 4 41 0 2 282
UK human 2014, 2015, 2016 596 29 273 0 117 177
DE food 2014, 2015, 2016 193 0 3 0 0 190
DE human 2014, 2015, 2016 166 0 5 0 0 161
FR animal 2010–2015 71 0 2 0 0 69
FR environmental 2010–2015 34 0 0 5 0 29