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Table 1 Validation of ISMapper using simulated reads

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

Isolate Accession IS Found Orientation
S. Typhi CT18 NC_003198 IS200 26/26 26/26
  IS1 3/3 3/3
S. Typhimurium LT2 NC_003197 IS200 6/6 6/6
  ISSty2b (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
  ISEc1b (1) 4/4 4/4
  ISEc8a 9/10 9/10
  1. aindicates ISMapper was unable to resolve some IS positions due to repeat regions
  2. bindicates ISMapper incorrectly identified an insertion site, the number of these sites are indicated in brackets