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

BMC Genomics

Table 1 Validation of ISMapper using simulated reads

Isolate	Accession	IS	Found	Orientation
S. Typhi CT18	NC_003198	IS200	26/26	26/26
S. Typhi CT18		IS1	3/3	3/3
S. Typhimurium LT2	NC_003197	IS200	6/6	6/6
		ISSty2^{b (1)}	2/2	2/2
		IS1351 ^{b (2)}	2/2	2/2
S. Typhi plasmid pHCM1	NC_003384	IS26	4/4	4/4
		ISVsa5	2/2	2/2
		IS1	5/5	5/5
S. Paratyphi plasmid pAKU_1	AM412236	IS26	5/5	5/5
		ISVsa5	2/2	2/2
		IS1	7/7	7/7
K. pneumoniae plasmid pNDMAR	JN420336	IS3000	3/3	3/3
		IS26 ^a	3/5	3/5
		ISEcp1	2/2	2/2
Yersinia pestis C092	NC_003143	IS100 ^a	43/44	43/44
		IS1661 ^{a, b (1)}	7/8	7/8
		IS1541 ^a	61/64	61/64
Escherichia coli O104:H4	NC_018658	IS1	10/10	10/10
		IS421	4/4	4/4
		IS609	4/4	4/4
		ISEc1	4/4	4/4
		ISKpn26	4/4	4/4
E. coli O157:H7	NC_002695	IS629 ^{a, b (1)}	17/18	17/18
		IS609	2/2	2/2
		ISEc1^{b (1)}	4/4	4/4
		ISEc8^a	9/10	9/10

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

ISSN: 1471-2164