Table 2 General features of the six S. enterica serovar Typhimurium genomes sequenced in this study
Strain (phage type) | L796 (DT99) | L847 (DT197) | L852 (DT135a) | L904 (DT9) | L927 (DT12a) | L945 (DT108) |
|---|---|---|---|---|---|---|
Total no. of reads | 8,204,694 | 13,168,608 | 8,746,596 | 8,844,626 | 7,363,632 | 8,894,448 |
Total sequences (bp) | 434,848,782 | 697,936,224 | 463,569,588 | 468,765,178 | 390,272,496 | 471,405,744 |
Coverage depth average | 69 | 121.1 | 62.7 | 63.6 | 62.9 | 73.2 |
Coverage depth range | 1-541 | 1-581 | 1-662 | 1-628 | 1-477 | 1-594 |
Percentage match to LT2 chromosome* | 96 | 96 | 96 | 96 | 98 | 91 |
Percentage match to LT2 pSLT* | 96 | 96 | 86 | 90 | 0.8 | 2.6 |
SNP sites (by BWA) | 3,323 | 2,268 | 2,615 | 2,545 | 2,616 | 2,422 |
SNP sites (by SOAP/progressiveMauve) | 2,477 | 1,349 | 2,862 | 3,089 | 1,349 | 1,866 |
No. and % of nSNP# | 391 (42.4) | 261 (42.4) | 224 (42.1) | 311 (46.8) | 250 (46.1) | 170 (43.5) |
No. and % of sSNP# | 327 (35.5) | 232 (37.7) | 200 (37.6) | 216 (32.5) | 200 (36.9) | 145 (37.1) |
No. and % of Intergenic SNPs# | 172 (18.7) | 108 (17.6) | 95 (17.9) | 123 (18.5) | 84 (15.5) | 67 (17.1) |
No. and % of single base deletions# | 32 (3.5) | 14 (2.3) | 13 (2.4) | 14 (2.1) | 8 (1.5) | 9 (2.3) |
Total SNPs | 922 | 615 | 532 | 664 | 542 | 391 |