Table 2.
SNP Annotations for Clade A and Clade B as Determined by kSNP
| kSNP Locus ID | Annot. | aa Change | Codon Change | Pos. in CDS | AE006468 Location | Gene | Locus Tag | Strand | Product Name |
|---|---|---|---|---|---|---|---|---|---|
| Clade B SNPs | |||||||||
| 115230 | Coding | A_A | GCC_GCG | 345 | 2417643 | STM2310 | − | Isochorismate synthase | |
| 139194 | Coding | P_P | CCC_CCG | 90 | 729566 | gltI, menF | STM0665 | − | Glutamate/aspartate transporter |
| 198788 | Coding | S_S | AGC_AGT | 126 | 2402046 | yfaZ | STM2294 | − | Putative inner membrane protein |
| 22659 | Coding | V_V | GTC_GTT | 125 | 1784052 | sapA | STM1692 | + | ABC superfamily peptide transport protein |
| 245765 | Coding | V_V | GTC_GTT | 206 | 1276770 | plsX | STM1192 | + | Putative fatty acid/phospholipid synthesis protein |
| 2656 | Coding | T_T | ACC_ACT | 57 | 17316 | STM0017 | − | Putative protein | |
| 266398 | Coding | A_A | GCC_GCT | 30 | 1518497 | STM1441 | − | Putative inner membrane protein | |
| 267325 | Coding | L_L | CTG_TTG | 370 | 552354 | fsr | STM0493 | − | Putative MFS family of transport protein |
| 34745 | Intergenic | 80406 | + | Upstream of STM0068, transcriptional regulator | |||||
| 365928 | Intergenic | 1332201 | + | Upstream of STM1246, reduced macrophage survival protein | |||||
| 370045 | Coding | S_S | TCA_TCG | 460 | 2727192 | lepA | STM2583 | − | GTP-binding elongation factor |
| 389879 | Coding | I_I | ATC_ATT | 97 | 729545 | gltI | STM0665 | − | Glutamate/aspartate transporter |
| 407961 | Coding | A_T | ACG_GCG | 26 | 2929670 | mig-14 | STM2782 | + | Putative transcription activator |
| 421386 | Coding | P_P | CCC_CCT | 43 | 2022982 | yecG | STM1927 | + | Putative universal stress protein |
| 444415 | Coding | V_V | GTA_GTT | 109 | 4820845 | yhhI | STM4566 | − | Putative cytoplasmic protein |
| 457785 | Intergenic | 3515395 | + | Upstream of STM3348, serine endoprotease | |||||
| 461849 | Coding | T_T | ACC_ACT | 26 | 2438962 | nuoB | STM2327 | − | NADH dehydrogenase I chain B |
| 559334 | Coding | G_G | GGG_GGT | 294 | 1524368 | tyrS | STM1449 | + | Tyrosine tRNA synthetase |
| 572551 | Coding | T_T_T | ACA_ACC_ACT | 650 | 2618849 | rihC | STM2503 | − | Putative diguanylate cyclase |
| 609237 | Coding | P_P | CCA_CCG | 13 | 60202 | mig-14 | STM0051 | + | Putative purine nucleoside hydrolase |
| 631239 | Coding | E_K | AAA_GAA | 56 | 2929760 | STM2782 | + | Putative transcription activator | |
| 632030 | Coding | A_A_A | GCA_GCC_GCT | 502 | 132233 | leuA | STM0113 | − | 2-isopropylmalate synthase |
| 647650 | Intergenic | 1528293 | − | Upstream of STM1542, putative POT family peptide transport protein | |||||
| 78823 | Coding | L_L | TTA_TTG | 41 | 1832990 | cls | STM1739 | + | Cardiolipin synthase |
| Clade A SNPs | |||||||||
| 135358 | Intergenic | 2449145 | + | Upsteam of STM2338, phosphotransacetylase | |||||
| 267325 | Coding | L_L | CTG_TTG | 370 | 552354 | fsr | STM0493 | − | Putative MFS family of transport protein |
| 271444 | Coding | Y_Y | TAC_TAT | 279 | 59782 | STM0050 | + | Putative nitrite reductase | |
| 370045 | Coding | S_S | TCA_TCG | 460 | 2727192 | lepA | STM2583 | − | GTP-binding elongation factor |
| 510549 | Coding | D_N | AAC_GAC | 144 | 2401994 | yfaZ | STM2294 | − | Putative inner membrane protein |
| 572551 | Coding | T_T_T | ACA_ACC_ACT | 650 | 2618849 | STM2503 | − | Putative diguanylate cyclase | |
Note.—SNPs that produce nonsynonymous amino acid substitutions are highlighted in Bold.