Table 3. Read mapping of sequenced qPCR amplicons.
| Highest% mapped | 2nd Highest% mapped* | |||
|---|---|---|---|---|
| Input | Genus | % Mapped Reads | Genus | % Mapped Reads |
| E. coli | Escherichia/Shigella | 98.03 | - | - |
| E. coli | Escherichia/Shigella | 92.59 | Vibrio | 3.10 |
| E. coli | Escherichia/Shigella | 94.96 | Vibrio | 1.76 |
| K. pneumoniae | Klebsiella | 77.99 | Enterobacter | 11.92 |
| K. pneumoniae | Klebsiella | 82.78 | Enterobacter | 8.34 |
| K. pneumoniae | Klebsiella | 79.48 | Enterobacter | 10.28 |
| A. baumannii | Acinetobacter | 99.95 | - | - |
| A. baumannii | Acinetobacter | 99.78 | - | - |
| A. baumannii | Acinetobacter | 99.09 | - | - |
| S. aureus | Staphylococcus | 99.70 | - | - |
| S. aureus | Staphylococcus | 99.17 | - | - |
| S. aureus | Staphylococcus | 99.93 | - | - |
| E. faecium | Enterococcus | 99.04 | - | - |
| E. faecium | Enterococcus | 98.32 | - | - |
| E. faecium | Enterococcus | 98.86 | - | - |
| P. aeruginosa | Pseudomonas | 99.89 | - | - |
| P. aeruginosa | Pseudomonas | 99.16 | - | - |
| P. aeruginosa | Pseudomonas | 99.83 | - | - |
| Enterobacter cloacae | Enterobacter | 85.49 | - | - |
| Enterobacter aerogenes | Enterobacter | 66.07 | Raoultella | 10.15 |
| Citrobacter freundii | Citrobacter | 88.76 | Kluyvera | 5.67 |
| Citrobacter koseri | Citrobacter | 75.66 | Salmonella | 15.00 |
| Proteus stuartii | Proteus | 86.64 | Vibrio | 5.74 |
| Serratia marcescens | Serratia | 77.69 | Vibrio | 21.15 |
| Klebsiella oxytoca | Enterobacter | 58.39 | Klebsiella | 25.82 |
| Proteus mirabilis | Proteus | 99.90 | - | - |
| Shigella sonnei | Escherichia/Shigella | 99.25 | - | - |
| Salmonella typhimurium | Salmonella | 98.34 | - | - |
| Salmonella senftenberg | Salmonella | 94.91 | Enterobacter | 3.76 |
* Only samples with less than 95% of reads mapped have a second genus shown