TABLE 3 

Unusual SNPs from various population genomic analyses

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