Table 5.
Non-synonymous, homozygous SNPs from independent clone pools of staphylococci after nisin selection.
| Gene ID (Prokka) | Protein ID | Pool | Position | Base change | Amino acid change | Allele frequency |
|---|---|---|---|---|---|---|
| S. aureus 171 | ||||||
| walk | WalK Sensor kinase | 1 | 17119 | A - > G | H364R | 1 |
| gltB_1 | Glutamate synthase | 1 | 437361 | A - > T | Q797L | 1 |
| rpoB | DNA-directed RNA polymerase subunit beta | 1 | 520176 | C - > T | H506Y | 1 |
| mraY | Phospho-N-acetylmuramoyl-pentapeptide transferase | 1 | 1103071 | G - > A | V266I | 1 |
| yhcF | Transcriptional regulator | 1 | 1998279 | G - > A | G73R | 1 |
| Hypothetical | Membrane protein | 2 | 615003 | C - > T | Q57∗ | 0.35 |
| rpoC | DNA-directed RNA polymerase subunit beta | 3 | 523690 | G - > T | A448S | 0.99 |
| femB | FemB | 3 | 1323450 | G - > A | R215H | 0.63 |
| Phage terminase | Terminase | 3 | 1491745 | G - > C | G240A | 1 |
| greA | GreA | 3 | 1625376 | A - > T | L76∗ | 0.37 |
| bras | BraS sensor histidine kinase | 3 | 2627088 | C - > T | T175I | 1 |
| S. hominis J31 | ||||||
| rpoB | DNA-directed RNA polymerase subunit beta | 1 | 41317 | G - > T | D1046Y | 0.79 |
| graS | GraS sensor histidine kinase | 2 | 147503 | C - > T | S120L | 0.42 |
| ftsH | FtsH Zinc metalloprotease | 2 | 2172470 | C - > A | D171E | 1 |
| gmk | Guanylate Kinase | 3 | 552630 | G - > A | R135H | 1 |
| yhcF | Transcriptional regulator | 3 | 1212777 | C - > T | Q47∗ | 1 |
| S. saprophyticus 883 | ||||||
| graS | GraS sensor histidine kinase | 1 | 2068987 | G - > T | G209C | 1 |
| codY | CodY regulator | 2,3 | 1537681 | C - > A | L79F | 1,1 |
| pitA | Phosphate transporter | 2,3 | 2066724 | C - > T | A195V | 0.99,1 |
| graS | GraS sensor histidine kinase | 2,3 | 2069134 | C - > A | R160S | 1,1 |
| marR family | MarR regulator | 2,3 | 2136907 | C - > T | T62I | 1,1 |
Names and functions of genes containing SNPs in the sequenced clone pools are shown with their locations and nucleotide change. Cognate amino acid change or stop (∗) is indicated. Pools comprised 5 clones from each of three independent experiments and allele frequencies were determined from numbers of corresponding reads in these pools. Nisin MICs of clones in each pool were confirmed to ensure they were similar.