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Table 2 Whole genome sequencing results

From: Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice

SRA accession numbera Mouse ID Sample Clone WITS ID WITS prevalence SNPb Coordinates in ST4/74 genomec Gene affected and amino acid effectd,e
SAMN04230908 5A Feces, 6 weeks 2A 7 63 % G- > T 1895850 kdgR, V61L
SAMN04230909 5B Feces, 4 weeks 1A 4 >96 % A- > G G- > A 22493 2578136 Synonymous, located in STM474_0020 Synonymous, located in maeB
SAMN04230910 5C Feces, 6 weeks 2A 7 88 % G- > T 1895850 kdgR, V61L
SAMN04230911 5D Feces, 4 weeks 1A 7 96 % G- > T 1895850 kdgR, V61L
SAMN04230912 5E Spleen 1A 1 63 % Deletion, T A- > G 3962521 63854 Promoter region of yicE Synonymous, located in STM474_0057
SAMN04230913 5E Liver 1A 3 98 % C- > A 3507750 ptsN, S21R
SAMN04230914 5E Feces, 6 weeks 1A 3 >98 % C- > A 3507750 ptsN, S21R
  1. aShort Read Archive database accession numbers for the raw sequencing reads
  2. bSingle nucleotide polymorphisms
  3. cAccession numbers NC_016857, CP002488-CP002490 [25]
  4. dGenes are denoted by their common name or by their STM474 gene number
  5. eAmino acids are denoted by their single letter code