<p>Table S5. Details of all variants discovered. Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 26 C T SNP Non-synonymous SAS0218 GGT PTS family glucose/glucoside 01 (glc) porter component IIABC 92 P 33 G C SNP Non-synonymous SAS0289 GGT Indigoidine synthase A-like 49 protein 75 P 34 G T SNP Non-synonymous SAS0299 GCT NADH:flavin oxidoreductase / 73 NADH oxidase family protein 08 P 41 C T SNP Synonymous SAS0365 GCC Xanthine permease 01 55 P 51 G A SNP Non-synonymous SAS0458 GGC 50S ribosomal protein 38 L25/general stress protein Ctc 65 P 52 G T SNP Non-synonymous SAS0462 GGT Tetrapyrrole methylase 04 03 P 52 A G SNP Non-synonymous SAS0467 AAA Hypoxanthine 43 phosphoribosyltransferase 33 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 54 A * Deletion Frameshift SAS0476 Putative pyridoxine 76 –A No premature stop biosynthesis protein 72 P 57 T C SNP Synonymous SAS0500 TAT DNA-directed RNA 13 polymerase subunit beta 02 P 10 C A SNP Premature stop SAS0973 TCA Iron compound ABC 43 transporter, iron compound- 15 binding protein 0 P 11 T C SNP Non-synonymous SAS1074 CAA Ribonuclease HIII 48 39 1 P 12 A G SNP Non-coding Intergenic Flanked by ribosome recycling 77 factor and undecaprenyl 31 diphosphate synthase 1 P 13 G A SNP Non-synonymous SAS1258 GAT Cardiolipin synthetase 47 05 8 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 14 G A SNP Premature stop SAS1361 CAA Acetyltransferase, GNAT 58 family 12 1 P 15 T C SNP Synonymous SAS1401 GAA Glycosyltransferase 26 09 0 P 15 C T SNP Non-coding Intergenic Flanked by hypothetical protein 50 and ferredoxin 31 8 P 15 A * Deletion Frameshift SAS1429 Hypothetical protein 55 –A Premature stop 91 5 P 15 G A SNP Non-synonymous SAS1462 ACG Exodeoxyribonuclease VII 89 large subunit 35 8 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 16 G C SNP Non-synonymous SAS1501 CGT Hypothetical protein 24 04 6 P 17 T C SNP Non-synonymous SAS1653 CAA Putative acyltransferase 87 93 1 P 18 A G SNP Non-synonymous SAS1661 GAG Acetoin utilization protein 00 AcuC 94 4 P 20 C A SNP Non-synonymous SAS1945 CAA Fructokinase, putative 90 84 8 P 21 C A SNP Non-coding Intergenic Flanked by ABC transporter, 00 ATP-binding protein and a 13 poor match CDS 7 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 21 C T SNP Synonymous SAS1959 CAC Acetolactate synthase large 07 subunit 97 3 P 22 G A SNP Non-synonymous SAS2082 CGC Aerobactin/siderophore 52 biosynthesis protein 77 7 P 22 T C SNP Synonymous SAS2117 TTA 30S ribosomal protein S13 87 13 4 P 23 T A SNP Non-coding Intergenic Flanked by inositol 58 monophosphatase family 57 protein and DeoR family 8 regulatory protein P 23 C T SNP Non-coding Intergenic Flanked by hypothetical protein 89 and DNA-3-methyladenine 91 glycosylase 1 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 24 C T SNP Premature stop SAS2271 CAA AraC family transcriptional 30 regulator 18 3 P 26 C T SNP Non-synonymous SAS2496 CTT Hypothetical protein 74 27 4 P 27 G A SNP Non-synonymous SAS2534 GCA Glycosyltransferase 28 27 2 P 27 C ATC Insertion Non-coding Intergenic Flanked by putative DNA- 85 +AT binding protein and putative 20 nickel transport protein 0 P 55 T C SNP Non-coding Intergenic Flanked by origin of replication 29b and beta-lactamase repressor ,c BlaI Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e P 23 T AT Insertion Non-coding Intergenic Flanked by alpha-acetolactate 50 +A synthase and conserved 67 hypothetical protein 7d Q 34 T A SNP Non-coding Intergenic 82 Q 11 AAG A Deletion Non-coding Intergenic 93 AAG –AGAAG 50 Q 12 A C SNP Non-coding Intergenic 91 65 Q 21 C T SNP Synonymous SAS0183 TTC Putative transport system 36 permease 33 Q 29 AAT A Deletion Frameshift SAS0250 Putative transport protein 54 AT –ATAT Premature stop 53 Q 33 A AA Insertion Frameshift SAS0286 ABC transporter ATP-binding 14 +A Premature stop protein 40 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 44 G A SNP Non-synonymous SAS0397 AGT Hypothetical protein 32 06 Q 46 T G SNP Synonymous SAS0415 GTT Hypothetical protein 15 33 Q 47 G A SNP Non-synonymous SAS0424 GGT MutT domain-containing 06 protein 77 Q 47 C T SNP Synonymous SAS0424 CGC MutT domain-containing 08 protein 98 Q 47 A G SNP Non-synonymous SAS0429 TAC Glutamate synthase, large 79 subunit 36 Q 50 G T SNP Non-synonymous SAS0442 AGG Hypothetical protein 00 08 Q 52 G A SNP Non-coding Intergenic 46 77 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 55 C T SNP Premature stop SAS0481 CAA ATP:guanido 12 phosphotransferase 49 Q 55 C T SNP Non-synonymous SAS0481 ACA ATP:guanido 15 phosphotransferase 44 Q 58 T G SNP Non-coding Intergenic 82 39 Q 66 T A SNP Non-synonymous SAS0592 TTA Putative monovalent cation/H+ 83 antiporter subunit D 89 Q 70 G T SNP Non-synonymous SAS0625 GCG Putative sensor histidine kinase 30 protein 77 Q 78 T C SNP Non-synonymous SAS0706 GTA Hypothetical protein 84 47 Q 10 G T SNP Non-synonymous SAS0962 AGT Hypothetical protein 34 60 2 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 10 G A SNP Non-synonymous SAS0985 TCT Putative aminotransferase 54 61 2 Q 10 G A SNP Non-coding Intergenic 56 76 2 Q 11 A G SNP Non-synonymous SAS1060 GTT Hypothetical protein 33 68 9 Q 11 G T SNP Non-synonymous SAS1078 TTG Recombination and DNA 53 strand exchange inhibitor 19 protein 5 Q 12 T A SNP Non-coding Intergenic 86 91 6 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 14 T G SNP Non-synonymous SAS1327 GAT ABC transporter ATP-binding 22 protein 02 7 Q 14 A T SNP Synonymous SAS1328 GTT ABC transporter permease 23 protein 37 1 Q 15 C G SNP Synonymous SAS1454 GCG Lipoamide acyltransferase 81 component of branched-chain 91 alpha-keto acid dehydrogenase 4 complex Q 16 C T SNP Synonymous SAS1482 CAG Hypothetical protein 05 63 0 Q 16 C T SNP Non-synonymous SAS1574 GGT Hypothetical protein 99 00 5 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 17 A G SNP Synonymous SAS1604 AAT Trigger factor 27 04 3 Q 18 A T SNP Non-synonymous SAS1682 TTT Putative surface anchored 26 protein 16 1 Q 18 G A SNP Non-synonymous SAS1682 ACA Putative surface anchored 31 protein 87 3 Q 18 C T SNP Non-synonymous SAS1682 GGA Putative surface anchored 32 protein 18 8 Q 19 T C SNP Synonymous SAS1823 CCA Aspartyl/glutamyl-tRNA 84 amidotransferase subunit A 10 5 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 21 A C SNP Non-coding Intergenic 86 04 8 Q 22 T A SNP Non-coding Intergenic 05 17 4 Q 22 T A SNP Non-coding Intergenic 05 17 5 Q 22 T A SNP Non-coding Intergenic 05 18 2 Q 22 T TT Insertion Non-coding Intergenic 55 +T 27 2 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 22 C T SNP Synonymous SAS2103 ATC Hyaluronate lyase precursor 2 73 88 1 Q 22 G T SNP Non-synonymous SAS2103 ATG Hyaluronate lyase precursor 2 74 46 0 Q 24 C G SNP Non-coding Intergenic 32 65 7 Q 25 A T, G SNP Non-synonymous SAS2383 AAA Putative cell wall-anchored 52 protein 92 0 Q 26 G A SNP Non-synonymous SAS2489 TCC 4-aminobutyrate 66 aminotransferase 83 4 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e Q 26 A G SNP Synonymous SAS2501 GAT Choline transporter 80 87 7 Q 41 Deletion Large deletion Partial match to MRSA252 37 –8kb pathogenicity island SaPI4 38- 42 10 47e Q 86 Deletion Large deletion Integrase 83 –1.6kb 89- 86 95 68f R 31 C T SNP Non-synonymous SAS0023 GCT Putative 5'-nucleotidase 51 7 R 18 C T, G SNP Non-coding Intergenic 21 41 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 19 C A SNP Synonymous No match CGC 18 83 R 22 C A SNP Non-coding Intergenic 98 55 R 25 G A SNP Premature stop SAS0218 CAA Putative PTS transport system, 95 IIBC component 39 R 26 C T SNP Non-synonymous SAS0223 CCT Putative PTS transport system, 61 IIC component 63 R 27 T G SNP Synonymous SAS0228 GGT Putative zinc-binding 09 dehydrogenase 01 R 29 G C, A SNP Synonymous SAS0248a GTG Hypothetical protein 39 61 R 42 T G SNP Synonymous SAS0385 GGT Superantigen-like protein 90 86 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 45 C T SNP Non-synonymous SAS0410 GCA NADH dehydrogenase subunit 60 5 03 R 56 T C SNP Non-synonymous SAS0486 GTG Serine acetyltransferase 00 32 R 56 A AA Insertion Non-coding Intergenic 68 +A 74 R 58 A G SNP Synonymous SAS0511 GCA Hypothetical protein 74 39 R 63 T C SNP Non-coding Intergenic 57 56 R 69 C CC Insertion Non-coding Intergenic 97 +C 16 R 74 T C SNP Non-coding Intergenic 72 66 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 75 C T SNP Synonymous SAS0679 GGC Para-aminobenzoate synthase 67 component 65 R 80 T G SNP Non-coding Intergenic 05 21 R 81 G T SNP Non-synonymous SAS0727 GTT Putative acetyltransferase 45 79 R 83 T A SNP Non-synonymous SAS0746 GAT Ribonuclease R 57 01 R 11 A C SNP Synonymous SAS1047 CTA Hypothetical protein 19 22 3 R 11 C T SNP Synonymous SAS1075 CTA Hypothetical protein 49 70 1 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 12 G A SNP Non-synonymous SAS1164 AGC Malonyl CoA-acyl carrier 42 protein transacylase 68 4 R 12 T A SNP Synonymous SAS1201 ATT Hypothetical protein 88 85 9 R 12 T C SNP Synonymous SAS1203 CGT Translation initiation factor IF- 90 2 08 0 R 14 A G SNP Synonymous SAS1337 CTA Dihydrodipicolinate reductase 33 55 5 R 14 T TT Insertion Frameshift SAS1346 Hypothetical protein 40 +T Premature stop 65 5 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 14 C A SNP Non-synonymous SAS1872 GAG Enterotoxin type A precursor 41 36 8 R 14 T A, C SNP Non-synonymous SAR1447g AAT Very large surface anchored 81 protein 69 8 R 15 C A SNP Non-synonymous SAS1389 GTT Hypothetical protein 12 66 1 R 16 T TT Insertion Non-coding Intergenic 66 +T 24 0 R 17 C T SNP Non-synonymous SAS1615 GGC Glyceraldehyde 3-phosphate 38 dehydrogenase 2 38 5 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 18 T G SNP Synonymous SAS1684 GCA Leucyl-tRNA synthetase 35 25 7 R 19 G A SNP Non-synonymous SAS1787 GAT Hypothetical protein 48 66 4 R 19 T G SNP Non-synonymous SAS1791 GTT Hypothetical protein 53 85 8 R 20 TTT T Deletion Non-coding Intergenic 25 AGG –TTAG 57 GAC GGAC 8 TTT TTT R 21 TT T Deletion Frameshift SAS1968 Putative RNA binding protein 24 –T Premature stop 96 4 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 21 T C SNP Synonymous SAS2014 TCA UDP-GlcNAc 2-epimerase 68 89 3 R 23 A G SNP Non-coding Intergenic 64 63 3 R 23 AA A Deletion Non-coding Intergenic 89 –A 10 3 R 24 A G SNP Non-coding Intergenic 68 24 4 R 25 T C SNP Non-synonymous SAS2377 ACT Putative NUDIX hydrolase 44 13 8 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 26 AA A Deletion Non-coding Intergenic 03 –A 82 4 R 26 T C SNP Non-synonymous SAS2475 ATA Dihydroorotate dehydrogenase 52 2 93 1 R 26 T TT Insertion Frameshift SAS2498 Putative betaine aldehyde 77 +T Premature stop dehydrogenase 25 0 R 27 A T SNP Synonymous SAS2547 CGT Acetyltransferase (GNAT) 48 family protein 25 5 R 27 C A SNP Non-coding Intergenic 66 64 9 Parti- Po Ref Non- Type Effect CDS in MSSA476 Ref codon CDS functiona cipant siti Base ref on Base in M SS A4 76 ref ere nc e R 26 G A SNP Non-coding Intergenic 26 06 4e a As determined by BLAST and xbase for participant P and by xbase for participants Q and R. b Does not map to MSSA476. Position in plasmid pSAS (Genbank accession number BX571858). c Alternative annotation using MRSA252 reference: non-synonymous, TAC to CAC, SAR0710, hypothetical protein in integrated plasmid. d Does not map to MSSA476 or MRSA252. Position in Newman reference (Genbank accession number AP009351). e Does not map to MSSA476. Position in MRSA252. f Does not map to MSSA476. Position in Mu50 reference (Genbank accession number BA000017). g No annotated coding sequence in homologous position in MSSA476. CDS in MRSA252. Note that the positive strand is used to give Ref Base and Non-ref Base. The coding sequence reading frame may lie on the negative strand. Multiple non-reference bases occur when neither the ancestral or derived forms match the MSSA476 reference. No more than two alleles were detected within a single host at any site.</p>