breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 36,378 C→T L58L (TTG→TTA)  tpn ← IS431mec transposase
RA 1,416,458 A→T I216N (ATT→AAT)  oppD ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,513,930 A→T L413F (TTA→TTT)  USA300HOU_1379 → hypothetical membrane protein
RA 2,010,363 C→T C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,187,071 C→T R331K (AGA→AAA)  rsbU ← sigma factor B regulator
RA 2,279,705 G→A intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,532,298 A→T T15T (ACA→ACT)  murN → FemAB family peptidoglycan biosynthesis protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP000730 4556 4603 48 2 [1] [1] 2 recF recombination protein RecF
* * ÷ CP000730 14411 14487 77 2 [1] [1] 2 serS/azlC serine‑‑tRNA ligase/LIV‑E family branched chain amino acid exporter
* * ÷ CP000730 97901 97978 78 2 [1] [1] 2 dus possible tRNA‑dihydrouridine synthase
* * ÷ CP000730 155131 155244 114 2 [1] [1] 2 sasD cell wall surface anchor protein
* * ÷ CP000730 183362 183403 42 2 [1] [1] 4 cap5J capsular polysaccharide biosynthesis protein Cap5J
* * ÷ CP000730 257000 257095 96 2 [1] [1] 2 USA300HOU_0230 response regulator
* * ÷ CP000730 366310 366325 16 3 [1] [1] 2 USA300HOU_0334 SSS family solute:sodium (Na+) symporter
* * ÷ CP000730 464853 464918 66 2 [1] [1] 2 USA300HOU_0439 hypothetical protein
* * ÷ CP000730 525652 525737 86 2 [1] [1] 4 [metS] [metS]
* * ÷ CP000730 549247 549352 106 2 [1] [1] 2 ftsH cell division protein FtsH
* * ÷ CP000730 582984 583030 47 2 [1] [1] 2 [rplK] [rplK]
* * ÷ CP000730 611523 611555 33 2 [0] [1] 2 azo1/sdrC hypothetical protein/Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC
* * ÷ CP000730 623681 623768 88 2 [1] [1] 2 USA300HOU_0558 glycosyltransferase
* * ÷ CP000730 627682 627710 29 2 [1] [1] 2 USA300HOU_0561 hypothetical protein
* * ÷ CP000730 661760 661892 133 2 [1] [1] 2 USA300HOU_0603 hypothetical protein
* * ÷ CP000730 662004 662036 33 2 [1] [1] 2 USA300HOU_0603 hypothetical protein
* * ÷ CP000730 673708 673835 128 2 [1] [1] 2 [USA300HOU_0616] [USA300HOU_0616]
* * ÷ CP000730 727499 727581 83 2 [1] [1] 2 USA300HOU_0674 hypothetical protein
* * ÷ CP000730 734861 735040 180 3 [1] [1] 2 vraF possible ABC superfamily ATP binding cassette transporter, ABC protein
* * ÷ CP000730 755047 755175 129 2 [1] [1] 2 USA300HOU_0705 hypothetical protein
* * ÷ CP000730 785654 785729 76 3 [1] [1] 2 exsB ExsB family post‑transcriptional regulator
* * ÷ CP000730 795826 795965 140 2 [1] [1] 2 recQ1 ATP‑dependent helicase RecQ
* * ÷ CP000730 858492 858589 98 2 [1] [0] 2 pgk phosphoglycerate kinase
* * ÷ CP000730 881470 881546 77 2 [1] [1] 2 csp/USA300HOU_0825 cold‑shock protein/hypothetical protein
* * ÷ CP000730 904587 904668 82 2 [1] [1] 2 USA300HOU_0862 hypothetical protein
* * ÷ CP000730 917956 917998 43 2 [0] [1] 2 USA300HOU_0877/USA300HOU_0878 hypothetical membrane protein/CBS domain protein
* * ÷ CP000730 922734 922827 94 2 [1] [1] 2 yunD bifunctional 5‑nucleotidase/2,3‑cyclic phosphodiesterase
* * ÷ CP000730 935279 935407 129 2 [1] [1] 3 yutM hypothetical protein
* * ÷ CP000730 965521 965546 26 2 [1] [1] 2 rexB ATP‑dependent nuclease Rex subunit B
* * ÷ CP000730 1012454 1012542 89 2 [1] [1] 2 mgtE CPA2 family monovalent cation:proton (H+) antiporter‑2
* * ÷ CP000730 1012661 1012710 50 2 [1] [1] 2 mgtE CPA2 family monovalent cation:proton (H+) antiporter‑2
* * ÷ CP000730 1013847 1013900 54 2 [1] [1] 2 mgtE/USA300HOU_0968 CPA2 family monovalent cation:proton (H+) antiporter‑2/hypothetical protein
* * ÷ CP000730 1022978 1023041 64 2 [1] [1] 2 murE1 UDP‑N‑acetylmuramoylalanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase
* * ÷ CP000730 1026510 1026602 93 2 [1] [1] 2 ykoY hypothetical membrane protein
* * ÷ CP000730 1035051 1035128 78 2 [1] [1] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1041937 1042042 106 2 [1] [1] 2 USA300HOU_0984 glycosyltransferase
* * ÷ CP000730 1057231 1057335 105 2 [1] [1] 2 sspA/atl S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase
* * ÷ CP000730 1067804 1067874 71 2 [1] [1] 2 qoxB quinol oxidase subunit I
* * ÷ CP000730 1085363 1085540 178 2 [1] [1] 2 USA300HOU_1019 ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 1132673 1132769 97 2 [1] [1] 2 USA300HOU_1060 hypothetical protein
* * ÷ CP000730 1153515 1153624 110 2 [1] [1] 2 his2 MutS family DNA mismatch repair protein
* * ÷ CP000730 1161172 1161378 207 2 [1] [1] 2 sdhB1 succinate dehydrogenase iron‑sulfur subunit
* * ÷ CP000730 1213127 1213172 46 3 [1] [1] 2 carB carbamoyl‑phosphate synthase (glutamine‑hydrolyzing), large subunit
* * ÷ CP000730 1249048 1249055 8 2 [1] [0] 2 smc SMC superfamily ATP‑binding chromosome segregation protein
* * ÷ CP000730 1251831 1251880 50 2 [1] [1] 2 ftsY/yfhO Sec family Type I general secretory pathway protein signal recognition particle protein FtsY/hypothetical membrane protein
* * ÷ CP000730 1252022 1252071 50 2 [1] [1] 2 ftsY/yfhO Sec family Type I general secretory pathway protein signal recognition particle protein FtsY/hypothetical membrane protein
* * ÷ CP000730 1264599 1264664 66 2 [1] [1] 2 fmhC FemAB family peptidoglycan biosynthesis protein
* * ÷ CP000730 1267034 1267077 44 2 [1] [1] 2 topA DNA topoisomerase A
* * ÷ CP000730 1287124 1287260 137 2 [1] [1] 2 dnaE1 DNA‑directed DNA polymerase III alpha subunit
* * ÷ CP000730 1292977 1293063 87 2 [1] [1] 2 rbfA ribosome‑binding factor A
* * ÷ CP000730 1299815 1299851 37 2 [1] [1] 2 rnjB beta‑lactamase
* * ÷ CP000730 1307000 1307054 55 2 [1] [1] 2 USA300HOU_1213 hypothetical protein
* * ÷ CP000730 1331684 1331749 66 3 [1] [1] 2 miaA tRNA isopentenyltransferase
* * ÷ CP000730 1339251 1339335 85 2 [1] [1] 3 USA300HOU_1241/USA300HOU_1242 hypothetical protein/hypothetical protein
* * ÷ CP000730 1389440 1389500 61 2 [1] [1] 2 parC DNA topoisomerase (ATP‑hydrolyzing) ParC
* * ÷ CP000730 1397179 1397220 42 2 [1] [1] 2 fmtC lysyl transferase
* * ÷ CP000730 1405647 1405673 27 2 [0] [1] 2 trpE anthranilate synthase alpha subunit
* * ÷ CP000730 1417564 1417678 115 2 [1] [1] 2 oppD oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 1421761 1421875 115 2 [1] [1] 2 phoU possible PnaS family phosphate:sodium (Na+) symporter
* * ÷ CP000730 1447746 1447841 96 2 [1] [1] 2 yojN nitric‑oxide reductase
* * ÷ CP000730 1450136 1450279 144 2 [1] [1] 2 odhB dihydrolipoyllysine‑residue succinyltransferase
* * ÷ CP000730 1454332 1454447 116 3 [1] [1] 3 arlS sensor histidine kinase
* * ÷ CP000730 1458337 1458412 76 2 [1] [1] 2 [USA300HOU_1354]–[murG] [USA300HOU_1354],[murG]
* * ÷ CP000730 1466305 1466359 55 2 [1] [1] 2 [thyA] [thyA]
* * ÷ CP000730 1466532 1466550 19 2 [1] [1] 2 thyA/USA300HOU_1365 thymidylate synthase/hypothetical protein
* * ÷ CP000730 1470429 1470438 10 2 [1] [1] 2 rnhA possible ribonuclease H
* * ÷ CP000730 1483138 1483239 102 2 [1] [1] 2 ebh extracellular matrix binding protein
* * ÷ CP000730 1499059 1499101 43 2 [1] [1] 3 ebh extracellular matrix binding protein
* * ÷ CP000730 1507116 1507183 68 2 [1] [1] 2 ald1 alanine dehydrogenase
* * ÷ CP000730 1517578 1517596 19 2 [1] [1] 2 USA300HOU_1385 hypothetical protein
* * ÷ CP000730 1521716 1521756 41 2 [1] [1] 2 USA300HOU_1389 hypothetical protein
* * ÷ CP000730 1540179 1540206 28 2 [1] [1] 2 ndk/gerC nucleoside‑diphosphate kinase/trans‑hexaprenyltranstransferase subunit II
* * ÷ CP000730 1581718 1581750 33 2 [1] [1] 2 USA300HOU_1450 possible bacteriophage capsid protein
* * ÷ CP000730 1598391 1598410 20 2 [1] [1] 3 USA300HOU_1475 hypothetical bacteriophage protein
* * ÷ CP000730 1603479 1603505 27 2 [1] [1] 2 USA300HOU_1488/USA300HOU_1489 possible lipoprotein/hypothetical bacteriophage protein
* * ÷ CP000730 1626948 1627001 54 2 [1] [1] 2 USA300HOU_1511/pgd lactoylglutathione lysase/phosphogluconate dehydrogenase (decarboxylating)
* * ÷ CP000730 1634081 1634091 11 2 [0] [1] 2 yqiW 2‑oxoisovalerate dehydrogenase (acylating) beta subunit
* * ÷ CP000730 1697965 1698024 60 2 [1] [1] 2 holA possible DNA‑directed DNA polymerase III delta subunit
* * ÷ CP000730 1709715 1709772 58 2 [1] [1] 2 sem/USA300HOU_1604 enterotoxin/hypothetical protein
* * ÷ CP000730 1753402 1753452 51 2 [1] [1] 2 ruvA crossover junction endodeoxyribonuclease
* * ÷ CP000730 1760693 1760720 28 2 [1] [1] 2 radC DNA repair protein RadC
* * ÷ CP000730 1772855 1772949 95 2 [1] [1] 2 [hemX] [hemX]
* * ÷ CP000730 1788408 1788427 20 2 [1] [1] 2 nrdR/gapB hypothetical protein/glyceraldehyde‑3‑phosphate dehydrogenase (phosphorylating)
* * ÷ CP000730 1798110 1798139 30 2 [1] [1] 2 phoP response regulator
* * ÷ CP000730 1799485 1799549 65 2 [1] [1] 2 icd isocitrate dehydrogenase (NADP(+))
* * ÷ CP000730 1803006 1803085 80 2 [1] [1] 3 [cycA] [cycA]
* * ÷ CP000730 1817930 1817987 58 2 [1] [1] 2 [USA300HOU_1692] [USA300HOU_1692]
* * ÷ CP000730 1841388 1841472 85 2 [1] [1] 2 htrA S1 family peptidase
* * ÷ CP000730 1867434 1867508 75 2 [1] [1] 2 USA300HOU_1736 hypothetical protein
* * ÷ CP000730 1887148 1887152 5 2 [0] [1] 2 leuS leucine‑‑tRNA ligase
* * ÷ CP000730 1892660 1892715 56 2 [1] [1] 2 rot/USA300HOU_1755 repressor of toxins Rot/lysophospholipase
* * ÷ CP000730 1907061 1907099 39 2 [1] [1] 2 USA300HOU_1768/USA300HOU_1769 hypothetical protein/hypothetical protein
* * ÷ CP000730 1934701 1934764 64 2 [1] [1] 2 USA300HOU_1798 hypothetical protein
* * ÷ CP000730 1988758 1988795 38 2 [1] [1] 2 cspR TrmH family RNA methyltransferase
* * ÷ CP000730 2027323 2027368 46 2 [1] [0] 2 vraS sensor histidine kinase VraS
* * ÷ CP000730 2061007 2061021 15 2 [1] [1] 2 pncB/nos nicotinate phosphoribosyltransferase/nitric‑oxide synthase, oxygenase subunit
* * ÷ CP000730 2084168 2084331 164 2 [1] [1] 3 mapW2 cell surface protein MapW2
* * ÷ CP000730 2127089 2127148 60 3 [1] [1] 2 USA300HOU_2008/int hypothetical bacteriophage protein/bacteriophage integrase
* * ÷ CP000730 2198265 2198276 12 2 [0] [1] 2 kdpD sensor histidine kinase KdpD
* * ÷ CP000730 2327081 2327118 38 2 [1] [1] 2 lacG 6‑phospho‑beta‑galactosidase
* * ÷ CP000730 2335837 2335856 20 2 [1] [1] 2 npdA/USA300HOU_2192 Sir2 family NAD‑dependent deacetylase/hypothetical protein
* * ÷ CP000730 2351119 2351162 44 2 [1] [1] 3 USA300HOU_2207 hypothetical protein
* * ÷ CP000730 2377423 2377496 74 2 [1] [1] 2 glcU DMT superfamily drug/metabolite transporter
* * ÷ CP000730 2385076 2385115 40 2 [1] [1] 2 fmhB/USA300HOU_2245 peptidoglycan pentaglycine interpeptide biosynthesis protein FmhB/hypothetical protein
* * ÷ CP000730 2411918 2412015 98 2 [1] [1] 2 [USA300HOU_2277]–[sarY] [USA300HOU_2277],[sarY]
* * ÷ CP000730 2412234 2412239 6 2 [0] [1] 2 sarY staphylococcal accessory regulator Y
* * ÷ CP000730 2460248 2460264 17 2 [0] [1] 2 natB ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 2692235 2692333 99 2 [1] [0] 2 USA300HOU_2546 RND superfamily resistance‑nodulation‑cell division:proton (H+) antiporter
* * ÷ CP000730 2705123 2705174 52 2 [1] [1] 2 crtQ glycosyltransferase
* * ÷ CP000730 2732706 2732788 83 2 [1] [1] 2 USA300HOU_2590 possible S15 family peptidase
* * ÷ CP000730 2785563 2785614 52 2 [1] [1] 2 aur M04 family aureolysin

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =6 (0.770)11 (2.080)
+45 bp		 11/190 0.0 59.7% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 2176447 = 16 (2.040)noncoding (114/114 nt) rrf5 5S ribosomal RNA