ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

BMC Genomics

Table 2 Validation of ISMapper using real Illumina reads for which finished genomes were also available

Isolate	Genome accession	FastQ accession	IS	Found	Orientation
Streptococcus suis P1/7	AM946016	ERR225612	ISSu3	4/4	4/4
Streptococcus suis P1/7			ISSu4^{b (2)}	2/2	2/2
Staphylococcus aureus TW20	NC_017331	ERR043367	ISSep3	3/3	3/3
			IS256	8/8	8/8
			IS431mec^a	3/4	3/4
			IS1181	2/2	2/2
Klebsiella pneumoniae NJST258_1	CP006923	SRR1166975	ISKpn1	5/5	5/5
			IS5B	8/8	8/8
			IS903B^{b (1)}	2/2	2/2
			IS1294	3/3	3/3
			ISKpn18	2/2	2/2
			ISKpn26	7/7	7/7
S. Typhi CT18	NC_003198	ERR343331	IS200	26/26	26/26
S. Typhi CT18			IS1 ^a	2/3	2/3
S. Typhi Ty2	AE014613	ERR343332	IS200	26/26	26/26

^aindicates ISMapper was unable to resolve some positions due to repeat regions
^bindicates ISMapper incorrectly identified an insertion site, the number of these sites are indicated in brackets

ISSN: 1471-2164