| Coordinates | Strand | Length | PID | Gene name | Synonym | FunctionCode | COG | GCRegion | HGT | SimGC | SimMah | Dev.AA | Function |
| 33692..34171 | + | 477 | 15925729 | orfX | SA0023 | S | COG1576 | H | 2 | 2 | conserved hypothetical protein orfX | ||
| 40818..41588 | - | 768 | 15925740 | aadD | SA0033 | - | - | H | 2 | 2 | kanamycin nucleotidyltransferase | ||
| 44558..44986 | + | 426 | 15925744 | - | SA0037 | I | COG2030 | H | 1 | 2 | conserved hypothetical protein | ||
| 48895..49266 | + | 369 | 15925747 | mecI | SA0040 | - | - | H | 2 | 1 | methicillin resistance regulatory protein | ||
| 61583..62101 | - | 516 | 15925761 | - | SA0054 | - | - | H | 1 | 2 | hypothetical protein | ||
| 80857..81228 | + | 369 | 15925778 | kdpC(SCCmec) | SA0071 | P | COG2156 | H | 2 | 2 | potassium-transporting ATPase C chain homologue | ||
| 267216..268400 | - | 1182 | 15925934 | - | SA0223 | I | COG0183 | + | H | 2 | 0 | acetyl-CoA acetyltransferase homologue | |
| 268430..270691 | - | 2259 | 15925935 | - | SA0224 | I | COG1250 | + | H | 0 | 0 | hypothetical protein, similar to 3-hydroxyacyl-CoA dehydrogenase | |
| 270877..272088 | - | 1209 | 15925936 | - | SA0225 | I | COG1960 | + | H | 1 | 0 | hypothetical protein, similar to glutaryl-CoA dehydrogenase | |
| 272200..273705 | - | 1503 | 15925937 | - | SA0226 | I | COG0318 | + | H | 0 | 0 | hypothetical protein, similar to acid-CoA ligase | |
| 273731..275293 | - | 1560 | 15925938 | - | SA0227 | I | COG2057 | + | H | 0 | 0 | conserved hypothetical protein | |
| 278878..279234 | - | 354 | 15925941 | - | SA0230 | S | COG3189 | + | H | 0 | 2 | conserved hypothetical protein | |
| 320229..321179 | + | 948 | 15925978 | lytM | SA0265 | M | COG0739 | H | 2 | 1 | peptidoglycan hydrolase | ||
| 365435..367510 | + | 2073 | 15926022 | geh | SA0309 | R | COG1075 | + | H | 1 | 0 | glycerol ester hydrolase | |
| 368652..369851 | - | 1197 | 15926024 | - | SA0311 | C | COG1902 | + | H | 2 | 0 | hypothetical protein, similar to trimethylamine dehydrogenase (EC 1.5.99.7) | |
| 370153..371154 | + | 999 | 15926025 | - | SA0312 | C | COG2141 | + | H | 0 | 0 | hypothetical protein, similar to alkanal monooxygenase alpha chain | |
| 371188..371520 | + | 330 | 15926026 | - | SA0313 | E | COG0509 | + | H | 1 | 2 | hypothetical protein, similar to glycine cleavage system H protein | |
| 371521..372321 | + | 798 | 15926027 | - | SA0314 | S | COG2110 | + | H | 0 | 0 | conserved hypothetical protein | |
| 372308..373255 | + | 945 | 15926028 | - | SA0315 | - | - | + | H | 0 | 0 | hypothetical protein | |
| 420987..422510 | - | 1521 | 15926081 | ahpF | SA0365 | O | COG3634 | + | H | 1 | 0 | alkyl hydroperoxide reductase subunit F | |
| 422526..423095 | - | 567 | 15926082 | ahpC | SA0366 | O | COG0450 | + | H | 0 | 0 | alkyl hydroperoxide reductase subunit C | |
| 423587..424342 | + | 753 | 15926083 | - | SA0367 | C | COG0778 | + | H | 1 | 0 | hypothetical protein, similar to nitro/flavin reductase | |
| 424422..425810 | - | 1386 | 15926084 | - | SA0368 | R | COG1823 | + | H | 2 | 0 | hypothetical protein, similar to proton/sodium-glutamate symport protein | |
| 428308..429264 | - | 954 | 15926086 | - | SA0370 | - | - | + | H | 1 | 0 | conserved hypothetical protein | |
| 436136..436672 | - | 534 | 15926093 | - | SA0377 | - | - | H | 1 | 2 | hypothetical protein [Pathogenicity island SaPIn2] | ||
| 497451..498878 | + | 1425 | 15926151 | treP | SA0432 | G | COG1264 | + | H | 0 | 0 | PTS enzyme II, phosphoenolpyruvate-dependent, trehalose-specific | |
| 498942..500582 | + | 1638 | 15926152 | - | SA0433 | G | COG0366 | + | H | 1 | 0 | alpha-glucosidase | |
| 500607..501335 | + | 726 | 15926153 | - | SA0434 | K | COG2188 | + | H | 0 | 0 | hypothetical protein, simialr to trehalose operon transcriptional repressor | |
| 526353..526679 | + | 324 | 15926175 | spoVG | SA0456 | M | COG2088 | H | 1 | 2 | stage V sporulation protein G homologue | ||
| 537687..538079 | + | 390 | 15926184 | - | SA0465 | - | - | H | 1 | 2 | hypothetical protein, similar to cell-division initiation protein | ||
| 706027..706455 | + | 426 | 15926333 | - | SA0611 | - | - | H | 1 | 2 | hypothetical protein | ||
| 720393..720818 | + | 423 | 15926345 | - | SA0623 | - | - | H | 2 | 1 | hypothetical protein | ||
| 845005..845307 | - | 300 | 15926460 | - | SA0738 | - | - | H | 2 | 2 | hypothetical protein | ||
| 893294..893677 | + | 381 | 15926514 | - | SA0786 | - | - | H | 1 | 2 | conserved hypothetical protein | ||
| 957379..957750 | - | 369 | 15926574 | - | SA0844 | - | - | H | 1 | 1 | hypothetical protein | ||
| 1041581..1042063 | + | 480 | 15926650 | - | SA0916 | F | COG0041 | H | 1 | 1 | hypothetical protein, similar to phosphoribosylaminoimidazole carboxylase PurE | ||
| 1136386..1136736 | + | 348 | 15926742 | - | SA1004 | - | - | H | 1 | 2 | hypothetical protein, similar to fibrinogen-binding protein | ||
| 1310377..1310583 | + | 204 | 15926893 | - | SA1151 | - | - | - | H | 2 | 2 | +T 4.6 | hypothetical protein |
| 1311817..1312002 | + | 183 | 15926894 | - | SA1152 | - | - | - | H | 2 | 2 | hypothetical protein | |
| 1312745..1312996 | + | 249 | 15926895 | - | SA1153 | - | - | - | H | 2 | 2 | hypothetical protein | |
| 1313719..1313913 | + | 192 | 15926896 | - | SAS039 | - | - | - | H | 2 | 2 | hypothetical protein | |
| 1315752..1315949 | + | 195 | 15926898 | - | SAS040 | - | - | - | H | 2 | 2 | +ENT 4.2 3.3 3.1 | hypothetical protein |
| 1317671..1318570 | + | 897 | 15926900 | - | SA1156 | Q | COG1131 | - | H | 2 | 0 | ABC transporter (ATP-binding protein) homolog | |
| 1318539..1319270 | + | 729 | 15926901 | - | SA1157 | R | COG0842 | - | H | 1 | 0 | hypothetical protein, similar to ABC transporter integral membrane protein | |
| 1319274..1320365 | + | 1089 | 15926902 | - | SA1158 | T | COG0642 | - | H | 2 | 0 | hypothetical protein, similar to two-component sensor histidine kinase | |
| 1320362..1320964 | + | 600 | 15926903 | - | SA1159 | T | COG2197 | - | H | 0 | 0 | hypothetical protein, similar to two-component response regulator | |
| 1484206..1484550 | - | 342 | 15927027 | - | SA1279 | - | - | H | 1 | 1 | conserved hypothetical protein | ||
| 1489382..1489723 | - | 339 | 15927032 | - | SA1284 | - | - | H | 1 | 1 | hypothetical protein | ||
| 1603983..1604327 | - | 342 | 15927149 | - | SA1398 | M | COG0818 | H | 1 | 2 | hypothetical protein, similar to diacylglycerol kinase | ||
| 1627446..1628015 | - | 567 | 15927174 | - | SA1422 | H | COG1057 | H | 1 | 2 | conserved hypothetical protein | ||
| 1834047..1834517 | + | 468 | 15927351 | - | SA1595 | K | COG1595 | H | 1 | 1 | hypothetical protein | ||
| 1867585..1868058 | + | 471 | 15927391 | - | SA1635 | - | - | - | H | 2 | 0 | +N 3.5 | hypothetical protein [Pathogenicity island SaPIn3] |
| 1868063..1868854 | + | 789 | 15927392 | - | SA1636 | - | - | - | H | 1 | 0 | hypothetical protein [Pathogenicity island SaPIn3] | |
| 1869224..1870207 | - | 981 | 15927393 | lukD | SA1637 | - | - | - | H | 0 | 0 | leukotoxin, LukD [Pathogenicity island SaPIn3] | |
| 1870209..1871144 | - | 933 | 15927394 | lukE | SA1638 | - | - | - | H | 0 | 0 | leukotoxin LukE | |
| 1872508..1873296 | + | 786 | 15927395 | - | SA1639 | - | - | - | H | 2 | 0 | +N 3.0 | hypothetical protein [Pathogenicity island SaPIn3] |
| 1874130..1874624 | + | 492 | 15927396 | - | SA1640 | - | - | - | H | 0 | 2 | +N 6.1 | conserved hypothetical protein [Pathogenicity island SaPIn3] |
| 1874959..1875735 | + | 774 | 15927397 | - | SA1641 | - | - | - | H | 2 | 0 | hypothetical protein [Pathogenicity island SaPIn3] | |
| 1876287..1877063 | - | 774 | 15927398 | seg | SA1642 | - | - | - | H | 1 | 0 | extracellular enterotoxin type G precursor | |
| 1877346..1878122 | - | 774 | 15927399 | sen | SA1643 | - | - | - | H | 2 | 0 | enterotoxin SeN | |
| 1878140..1878550 | - | 408 | 15927400 | yent2 | SA1644 | - | - | - | H | 2 | 1 | enterotoxin YENT2 | |
| 1879065..1879793 | - | 726 | 15927402 | sei | SA1646 | - | - | - | H | 2 | 0 | extracellular enterotoxin type I precursor | |
| 1879828..1880547 | - | 717 | 15927403 | sem | SA1647 | - | - | - | H | 1 | 0 | enterotoxin SEM | |
| 1880828..1881610 | - | 780 | 15927404 | seo | SA1648 | - | - | - | H | 2 | 0 | enterotoxin SeO | |
| 1907077..1907472 | - | 393 | 15927426 | - | SA1670 | - | - | H | 1 | 2 | hypothetical protein | ||
| 1949094..1949480 | - | 384 | 15927461 | - | SA1703 | - | - | H | 2 | 1 | hypothetical protein | ||
| 1952403..1952855 | - | 450 | 15927464 | - | SA1706 | - | - | H | 2 | 2 | hypothetical protein | ||
| 1977295..1977621 | + | 324 | 15927484 | - | SA1726 | - | - | H | 2 | 1 | hypothetical protein | ||
| 1995011..1995568 | - | 555 | 15927501 | - | SA1741 | - | - | - | H | 1 | 0 | conserved hypothetical protein | |
| 1996902..1997642 | - | 738 | 15927504 | - | SA1744 | - | - | - | H | 2 | 0 | conserved hypothetical protein | |
| 1997642..1998514 | - | 870 | 15927505 | - | SA1745 | Q | COG1131 | - | H | 0 | 0 | hypothetical protein, similar to ABC transporter, ATP-binding protein | |
| 1998511..1999191 | - | 678 | 15927506 | - | SA1746 | - | - | - | H | 2 | 0 | hypothetical protein | |
| 2000723..2000899 | - | 174 | 15927509 | - | SAS057 | - | - | - | H | 2 | 2 | hypothetical protein | |
| 2003005..2003325 | - | 318 | 15927511 | truncated(mapW) | SA1751 | - | - | - | H | 2 | 2 | +K 3.5 | truncated map-w protein |
| 2003310..2004740 | - | 1428 | 15927512 | truncated(mapW) | SA1751 | - | - | - | H | 1 | 0 | truncated map-w protein | |
| 2033100..2033306 | - | 204 | 15927548 | - | SA1782 | - | - | + | H | 0 | 2 | +T 3.7 | hypothetical protein [Bacteriophage phiN315] |
| 2034118..2034366 | - | 246 | 15927551 | - | SA1785 | - | - | + | H | 1 | 2 | hypothetical protein [Bacteriophage phiN315] | |
| 2034378..2034626 | - | 246 | 15927552 | - | SA1786 | - | - | + | H | 1 | 2 | +Y 3.4 | hypothetical protein [Bacteriophage phiN315] |
| 2034623..2034880 | - | 255 | 15927553 | - | SA1787 | - | - | + | H | 1 | 2 | hypothetical protein [Bacteriophage phiN315] | |
| 2044270..2044533 | - | 261 | 15927572 | - | SA1804 | K | COG1396 | - | H | 2 | 1 | hypothetical transcriptional regulator [Bacteriophage phiN315] | |
| 2044667..2045380 | + | 711 | 15927573 | - | SA1805 | K | COG1396 | H | 1 | 2 | repressor homolog [Bacteriophage phiN315] | ||
| 2045396..2046328 | + | 930 | 15927574 | - | SA1806 | L | COG0847 | - | H | 2 | 0 | probable ATP-dependent helicase [Bacteriophage phiN315] | |
| 2046879..2047061 | + | 180 | 15927575 | - | SA1807 | - | - | - | H | 2 | 2 | +K 3.0 | hypothetical protein [Bacteriophage phiN315] |
| 2047161..2048144 | + | 981 | 15927576 | - | SA1808 | M | COG0463 | - | H | 2 | 0 | probable ss-1,3-N-acetylglucosaminyltransferase [Bacteriophage phiN315] | |
| 2048155..2048397 | + | 240 | 15927577 | - | SA1809 | - | - | - | H | 2 | 2 | +N 5.2 | hypothetical protein [Bacteriophage phiN315] |
| 2050616..2051632 | - | 1014 | 15927580 | - | SA1812 | - | - | - | H | 1 | 0 | hypothetical protein, similar to synergohymenotropic toxin precursor - Staphylococcus intermedius | |
| 2051654..2052709 | - | 1053 | 15927581 | - | SA1813 | - | - | - | H | 0 | 0 | hypothetical protein, similar to leukocidin chain lukM precursor | |
| 2054812..2056119 | + | 1305 | 15927583 | - | SA1815 | P | COG0168 | - | H | 1 | 0 | hypothetical protein, similar to Na+-transporting ATP synthase | |
| 2057136..2057858 | + | 720 | 15927584 | sel | SA1816 | - | - | - | H | 1 | 0 | extracellular enterotoxin L | |
| 2079423..2079986 | + | 561 | 15927611 | agrB | SA1842 | - | - | H | 2 | 1 | accessory gene regulator B | ||
| 2122977..2123336 | - | 357 | 15927646 | dpj | SA1875 | I | COG0736 | H | 1 | 2 | holo-ACP synthase | ||
| 2198285..2198758 | + | 471 | 15927721 | truncated-SA | SA1949 | - | - | H | 1 | 2 | lytic regulatory protein truncated with Tn554 | ||
| 2286486..2286809 | - | 321 | 15927792 | truncated-SA | SA2013 | L | COG1484 | H | 1 | 2 | truncated IS232 IstB protein homolog | ||
| 2342837..2343139 | + | 300 | 15927868 | ureA | SA2082 | E | COG0831 | H | 2 | 2 | urease gamma subunit | ||
| 2348074..2348421 | - | 345 | 15927875 | sarR | SA2089 | - | - | H | 2 | 2 | staphylococcal accessory regulator A homolog | ||
| 2428340..2428741 | - | 399 | 15927951 | - | SA2161 | K | COG0454 | H | 1 | 2 | hypothetical protein, similar to attachment to host cells and virulence | ||
| 2452690..2456379 | - | 3687 | 15927975 | narG | SA2185 | C | COG0243 | + | H | 1 | 0 | +W 3.1 | respiratory nitrate reductase alpha chain |
| 2456688..2457665 | - | 975 | 15927976 | nasF | SA2186 | H | COG0007 | + | H | 1 | 0 | uroporphyrin-III C-methyl transferase | |
| 2457656..2457970 | - | 312 | 15927977 | nasE | SA2187 | P | COG2146 | + | H | 0 | 2 | +C 4.4 | assimilatory nitrite reductase |
| 2460445..2461176 | - | 729 | 15927979 | - | SA2189 | S | COG2138 | + | H | 1 | 0 | hypothetical protein, simialr to NirR | |
| 2461406..2461942 | - | 534 | 15927980 | - | SA2190 | K | COG0454 | + | H | 0 | 0 | conserved hypothetcial protein | |
| 2540378..2540800 | - | 420 | 15928053 | - | SA2262 | S | COG2128 | H | 1 | 2 | conserved hypothetical protein | ||
| 2562947..2563306 | - | 357 | 15928077 | sarH3 | SA2286 | K | COG1846 | H | 2 | 2 | staphylococcal accessory regulator A homolog | ||
| 2607189..2607545 | - | 354 | 15928115 | - | SA2324 | O | COG0526 | H | 1 | 2 | hypothetical protein, similar to thioredoxin | ||
| 2660812..2661180 | - | 366 | 15928165 | - | SA2372 | - | COG0419 | H | 1 | 2 | hypothetical protein |
