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Table 1 S . Typhimurium isolates sequenced for this study

From: Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

Isolate Year Source (Outbreak) Mean depth Reads mapped Reads accession Contigs (Total bp) Assembly accession
STm1 2006 Farm A (investigation) 999x 99% SRR925393 119 (4,944,286) AMDX02
STm2 2005 Farm A (investigation) 366x 99% SRR926593 227 (5,019,159) AMDY01
STm3 2005 Food (OB2) 395x 99% SRR926594 106 (4,945,185) AMEB02
STm4 2007 Human case (sporadic) 335x 99% SRR926595 150 (4,968,080) AMEC02
STm5 2005 Human case (OB2) 1118x 99% SRR926602 458 (4,943,760) AMEH02
STm6 2008 Food (restaurant A, OB7) 302x 99% SRR926596 84 (4,938,199) AMED02
STm7 2008 Human case (restaurant A, OB7) 267x 99% SRR925415 117 (5,090,822) ATWR01
STm8 2005 Human case (OB1) 311x 99% SRR926597 102 (4,937,750) AMDZ02
STm9 2007 Human case (OB6) 350x 99% SRR926598 90 (4,932,393) AMEA02
STm10 2005 Human case (sporadic) 523x 99% SRR926599 104 (4,946,110) AMEE02
STm11 2005 Human case (OB5) 368x 99% SRR926600 118 (4,948,677) AMEF02
STm12 2008 Human case (restaurant A, OB7) 354x 99% SRR926601 262 (4,990,531) AMEG02
  1. Isolates studied were numbered STm1, STm2, up to STm12 and were all phage type 135@ (STm135@). OB = outbreak. Mapping statistics refer to mapping against the S. Typhimurium SL1344 reference chromosome (mean depth of mapped reads and proportion of total reads mapped to this reference).