Table 3.

The accuracy of ShigEiFinder with the identification dataset and validation dataset

ShigEiFinder assignments	Identification dataset (n=1969)*		Validation dataset (n=15501)
	Assembled genome	Read mapping	Assembled genome	Read mapping
Shigella or EIEC clusters	1871	1848	15455	15471
Multiple Shigella or EIEC clusters	9	6	33	7
Shigella or EIEC unclustered	0	8	13	23
Not Shigella /EIEC	89	89	0	0
Accuracy†	99.54%	99.28%	99.70%	99.81%

*Reads were not available for 18 EIEC isolates downloaded from NCBI in the identification dataset. The identification dataset has 90 non-Shigella/EIEC isolates including 72 ECOR isolates and 18 E.albertii isolates. One E. albertii isolate was assigned to SB13 by ShigaTyper which was grouped into cluster SB13 on the phylogenetic tree.

†Accuracy was defined as the number of Shigella and EIEC isolates being correctly assigned to a cluster over the total number tested.