TABLE 3 .
Unusual SNPs from various population genomic analyses
| Category and TCH1516a chromosome coordinate(s) |
TCH1516 locus, gene | Comment |
|---|---|---|
| SNPs that are polymorphic in both USA300-NAE and USA300-SAE clades |
||
| 460 | Intergenic before 0001 | |
| 14575 | Intergenic 0008–0009 | |
| 233245 | Coding 0210, hypothetical protein | nSNP |
| 2542210 | Intergenic 2401–2402 | |
| SNPs with derived allele present in ≥10 populations with ≥10% average frequency and a significant frequency gradient |
||
| 7282 | Coding 0006, gyrA | nSNP |
| 2708710 | Coding 2561, ssa-1 | sSNP |
| SNPs within intervals that were recombined more often than expected under the CFML recombination model |
||
| 168833–169219 | Intergenic 0159–0160 | Recombined on 3 or 4 branches |
| 672683–672727 | Intergenic 0614–0615 | Recombined on 3 or 4 branches |
| 2600705 | Intergenic 2461–2462 | Recombined on 3 branches |
| 2600727–2600792 | Intergenic 2461–2462 | Recombined on 3 or 4 branches |
| 2680141–2680194 | Intergenic 2536–2537 | Recombined on 8 or 9 branches |
| 2813570–2813582 | Coding 2564, sraP | Recombined on 4 branches |
a
The TCH1516 locus designation has the prefix USA300HOU_.