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 478,502 C→A D342E (GAC→GAA ndhF → NADH dehydrogenase (ubiquinone)
RA 584,121 G→T intergenic (+205/‑67) rplA → / → rplJ ribosomal protein L1/ribosomal protein L10
RA 707,909 A→T M1M (TTG→ATG) † mntB ← ABC superfamily ATP binding cassette transporter, ABC protein
RA 973,213 C→A E175* (GAG→TAG)  yitU ← possible HAD superfamily hydrolase
RA 1,002,200 T→G M173R (ATG→AGG)  mecA2 → competence negative regulator MecA
RA 1,105,994 T→C T12T (ACT→ACC pdhD → dihydrolipoyl dehydrogenase
RA 1,196,508 C→A intergenic (+2563/‑1229) ftsQ → / → ylmE cell division protein FtsQ/hypothetical protein
RA 1,232,053 A→T D233V (GAT→GTT)  prpC → possible PP2C protein phosphatase
RA 1,416,458 A→T I216N (ATT→AAT)  oppD ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,646,189 G→C A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,473 C→T A67T (GCT→ACT)  apt ← adenine phosphoribosyltransferase
RA 2,010,363 C→T C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,279,705 G→A intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,289,257 A→C V78G (GTA→GGA)  ybbP ← hypothetical membrane protein
RA 2,455,692 Δ1 bp coding (1210/1260 nt) USA300HOU_2315 → hypothetical membrane protein
RA 2,455,698 2 bp→AT coding (1216‑1217/1260 nt) USA300HOU_2315 → hypothetical membrane protein
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 58235 58411 177 2 [1] [1] 2 USA300HOU_0048/USA300HOU_0049 hypothetical membrane protein/hypothetical protein
* * ÷ CP000730 58679 59008 330 2 [1] [1] 2 USA300HOU_0049/USA300HOU_0050 hypothetical protein/hypothetical protein
* * ÷ CP000730 60664 60899 236 2 [1] [1] 2 [USA300HOU_0052]–[USA300HOU_0053] [USA300HOU_0052],[USA300HOU_0053]
* * ÷ CP000730 63568 63662 95 2 [1] [1] 2 speG/USA300HOU_0058 diamine N‑acetyltransferase/hypothetical protein
* * ÷ CP000730 70771 70869 99 2 [1] [1] 2 [arcB1]–[arcR] [arcB1],[arcR]
* * ÷ CP000730 85062 85096 35 2 [1] [1] 2 USA300HOU_0082/copB nickel (Ni2+)/peptide ABC superfamily ATP binding cassette transporter, ABC protein/P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter
* * ÷ CP000730 102210 102275 66 2 [1] [1] 2 ywqM/USA300HOU_0103 possible transcriptional regulator/hypothetical protein
* * ÷ CP000730 130935 130985 51 2 [1] [0] 2 sarH1/sirC staphylococcal accessory regulator H1/iron (Fe3+) ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 169548 169661 114 3 [1] [1] 2 USA300HOU_0160 hypothetical protein
* * ÷ CP000730 170862 170990 129 2 [1] [1] 2 USA300HOU_0160/adhE hypothetical protein/alcohol dehydrogenase
* * ÷ CP000730 174003 174107 105 2 [1] [1] 3 [cap5A] [cap5A]
* * ÷ CP000730 203151 203249 99 2 [1] [1] 2 [yweA] [yweA]
* * ÷ CP000730 330200 330284 85 2 [1] [1] 3 USA300HOU_0296/esxA hypothetical protein/ESAT‑6 family virulence protein
* * ÷ CP000730 345080 345089 10 3 [1] [0] 2 USA300HOU_0309 hypothetical membrane protein
* * ÷ CP000730 346023 346141 119 2 [1] [1] 2 [USA300HOU_0310] [USA300HOU_0310]
* * ÷ CP000730 349527 349836 310 2 [1] [1] 2 USA300HOU_0316/USA300HOU_0317 hypothetical protein/hypothetical protein
* * ÷ CP000730 372047 372110 64 2 [1] [1] 2 USA300HOU_0339/lip1 hypothetical membrane protein/triacylglycerol lipase
* * ÷ CP000730 430004 430070 67 2 [1] [1] 2 ahpC1/nfrA peroxiredoxin subunit C/possible FMN reductase
* * ÷ CP000730 443287 443338 52 2 [1] [1] 2 USA300HOU_0416/USA300HOU_0417 hypothetical protein/transposase
* * ÷ CP000730 444093 444182 90 2 [1] [1] 2 [USA300HOU_0419] [USA300HOU_0419]
* * ÷ CP000730 459969 460046 78 2 [1] [0] 2 hsdS1 type I site‑specific deoxyribonuclease specificity subunit
* * ÷ CP000730 491369 491459 91 2 [1] [1] 2 metQ/sle1 ABC superfamily ATP binding cassette transporter, binding protein/possible LysM family autolysin
* * ÷ CP000730 530650 530726 77 2 [1] [1] 2 veg/rplY hypothetical protein/ribosomal protein L25
* * ÷ CP000730 611553 611680 128 2 [1] [1] 2 azo1/sdrC hypothetical protein/Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC
* * ÷ CP000730 646919 647102 184 2 [1] [1] 2 lplA2/mvaK1 lipoate‑‑protein ligase A/mevalonate kinase
* * ÷ CP000730 654664 654795 132 2 [1] [1] 2 USA300HOU_0592 hypothetical protein
* * ÷ CP000730 658676 658790 115 2 [1] [1] 3 USA300HOU_0598 hypothetical protein
* * ÷ CP000730 659339 659416 78 2 [1] [1] 2 USA300HOU_0598/USA300HOU_0600 hypothetical protein/hypothetical protein
* * ÷ CP000730 661147 661190 44 2 [1] [1] 2 USA300HOU_0602 hypothetical protein
* * ÷ CP000730 661312 661475 164 2 [1] [1] 2 USA300HOU_0602 hypothetical protein
* * ÷ CP000730 672405 672466 62 2 [1] [1] 3 USA300HOU_0614/yvrC deoxyribonuclease (pyrimidine dimer)/iron (Fe3+) ABC superfamily ATP binding cassette transporter, binding protein
* * ÷ CP000730 677741 677870 130 2 [1] [1] 2 [USA300HOU_0620] [USA300HOU_0620]
* * ÷ CP000730 679437 679587 151 2 [1] [1] 2 sarA/USA300HOU_0623 staphylococcal accessory regulator A/hypothetical protein
* * ÷ CP000730 739958 740113 156 2 [1] [1] 2 pitA/sle1 possible PiT family inorganic phosphate transporter/possible LysM domain protein
* * ÷ CP000730 767395 767438 44 2 [1] [1] 2 [USA300HOU_0716] [USA300HOU_0716]
* * ÷ CP000730 831014 831181 168 2 [1] [1] 3 raiA/secA1 possible ribosome‑associated inhibitor protein Y/Sec family Type I general secretory pathway preprotein translocase subunit SecA
* * ÷ CP000730 871137 871322 186 2 [1] [1] 2 USA300HOU_0815/USA300HOU_0816 hypothetical lipoprotein/hypothetical protein
* * ÷ CP000730 879072 879133 62 2 [1] [1] 2 emp/USA300HOU_0822 extracellular matrix protein‑binding protein/hypothetical protein
* * ÷ CP000730 880029 880134 106 2 [1] [1] 2 USA300HOU_0822/nuc hypothetical protein/micrococcal nuclease
* * ÷ CP000730 886744 886858 115 2 [1] [1] 2 USA300HOU_0833/USA300HOU_0834 hypothetical protein/hypothetical protein
* * ÷ CP000730 888997 889121 125 2 [1] [1] 2 [USA300HOU_0837] [USA300HOU_0837]
* * ÷ CP000730 907236 907626 391 2 [1] [1] 2 [USA300HOU_0866] [USA300HOU_0866]
* * ÷ CP000730 908358 908476 119 2 [1] [1] 2 USA300HOU_0866/ear hypothetical protein/Ear protein
* * ÷ CP000730 928082 928107 26 2 [1] [1] 2 USA300HOU_0891 hypothetical protein
* * ÷ CP000730 951558 951575 18 2 [1] [0] 2 yqiG/rocD flavin reductase/ornithine‑‑oxo‑acid transaminase
* * ÷ CP000730 982245 982261 17 2 [1] [1] 2 USA300HOU_0937
USA300HOU_0938
hypothetical protein
hypothetical membrane protein
* * ÷ CP000730 982786 982992 207 2 [1] [1] 2 USA300HOU_0938 hypothetical membrane protein
* * ÷ CP000730 983048 983224 177 2 [1] [1] 2 USA300HOU_0938 hypothetical membrane protein
* * ÷ CP000730 987682 987803 122 3 [1] [0] 2 USA300HOU_0943 hypothetical membrane protein
* * ÷ CP000730 987952 988180 229 3 [1] [1] 2 [oppB1] [oppB1]
* * ÷ CP000730 1003391 1003504 114 2 [1] [1] 2 mecA2/pepF competence negative regulator MecA/M03 family oligopeptidase F
* * ÷ CP000730 1033714 1033793 80 2 [1] [1] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1035070 1035096 27 2 [1] [1] 3 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1036091 1036245 155 2 [1] [1] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1037670 1037804 135 2 [1] [1] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1041427 1041584 158 2 [0] [1] 2 USA300HOU_0984 glycosyltransferase
* * ÷ CP000730 1054527 1054746 220 2 [1] [0] 2 sspA/atl S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase
* * ÷ CP000730 1064469 1064890 422 2 [1] [1] 2 [brpA] [brpA]
* * ÷ CP000730 1102216 1102350 135 2 [1] [1] 2 [USA300HOU_1035] [USA300HOU_1035]
* * ÷ CP000730 1169465 1169542 78 2 [1] [1] 3 USA300HOU_1097/USA300HOU_1098 hypothetical protein/hypothetical protein
* * ÷ CP000730 1171489 1171798 310 2 [1] [0] 2 hly/USA300HOU_1100 alpha‑hemolysin/hypothetical protein
* * ÷ CP000730 1171898 1172018 121 2 [0] [1] 2 [USA300HOU_1100] [USA300HOU_1100]
* * ÷ CP000730 1175354 1175445 92 2 [1] [1] 2 USA300HOU_1105/arcB2 exotoxin/ornithine carbamoyltransferase
* * ÷ CP000730 1264993 1265088 96 2 [1] [1] 2 fmhC FemAB family peptidoglycan biosynthesis protein
* * ÷ CP000730 1295818 1295970 153 2 [1] [1] 3 rpsO/pnp ribosomal protein S15/polyribonucleotide nucleotidyltransferase
* * ÷ CP000730 1313316 1313384 69 2 [0] [1] 2 rny/USA300HOU_1219 possible hydrolase/hypothetical protein
* * ÷ CP000730 1317808 1317867 60 2 [1] [1] 2 [miaB] [miaB]
* * ÷ CP000730 1338944 1339263 320 2 [1] [1] 2 USA300HOU_1241/USA300HOU_1242 hypothetical protein/hypothetical protein
* * ÷ CP000730 1339316 1339701 386 2 [1] [1] 2 USA300HOU_1242 USA300HOU_1242
* * ÷ CP000730 1341230 1341475 246 3 [1] [1] 2 [USA300HOU_1245] [USA300HOU_1245]
* * ÷ CP000730 1354849 1354884 36 2 [0] [1] 2 USA300HOU_1269/USA300HOU_1270 hypothetical protein/hypothetical protein
* * ÷ CP000730 1357197 1357337 141 2 [1] [1] 2 [USA300HOU_1272]–[thrA] [USA300HOU_1272],[thrA]
* * ÷ CP000730 1456223 1456445 223 2 [1] [1] 2 arlR/USA300HOU_1351 response regulator/hypothetical protein
* * ÷ CP000730 1466487 1466596 110 2 [1] [1] 2 thyA/USA300HOU_1365 thymidylate synthase/hypothetical protein
* * ÷ CP000730 1507753 1507920 168 2 [1] [1] 2 ald1/polA alanine dehydrogenase/5'‑3' exonuclease
* * ÷ CP000730 1539230 1539342 113 2 [1] [1] 2 [USA300HOU_1405] [USA300HOU_1405]
* * ÷ CP000730 1562066 1562379 314 2 [1] [1] 2 lukS‑PV/USA300HOU_1432 Panton‑Valentine leukocidin subunit S/bacteriophage amidase
* * ÷ CP000730 1604582 1604654 73 2 [1] [1] 2 USA300HOU_1489/USA300HOU_1490 hypothetical bacteriophage protein/integrase
* * ÷ CP000730 1608900 1608979 80 2 [1] [0] 2 USA300HOU_1492/srrB possible lipoprotein/sensor histidine kinase SrrB
* * ÷ CP000730 1641817 1641913 97 2 [1] [1] 2 [xseA]–[nusB] [xseA],[nusB]
* * ÷ CP000730 1654327 1654411 85 2 [1] [0] 3 USA300HOU_1541 possible competence protein ComGF
* * ÷ CP000730 1656125 1656196 72 2 [0] [1] 2 pulF competence protein ComGB
* * ÷ CP000730 1665251 1665341 91 2 [1] [1] 2 sodA/zurR superoxide dismutase/Fur family transcriptional regulator
* * ÷ CP000730 1697780 1697820 41 2 [1] [1] 2 [holA] [holA]
* * ÷ CP000730 1708329 1708415 87 2 [1] [1] 2 USA300HOU_1602 hypothetical membrane protein
* * ÷ CP000730 1732833 1733158 326 2 [1] [1] 2 [USA300HOU_1624] [USA300HOU_1624]
* * ÷ CP000730 1774371 1774457 87 2 [1] [1] 2 hemA/engB glutamyl‑tRNA reductase/possible GTP‑binding protein
* * ÷ CP000730 1795927 1796008 82 2 [0] [1] 3 USA300HOU_1678/phoR hypothetical membrane protein/sensor histidine kinase
* * ÷ CP000730 1907772 1908008 237 2 [1] [1] 2 [USA300HOU_1769] [USA300HOU_1769]
* * ÷ CP000730 1923817 1923868 52 2 [1] [1] 2 USA300HOU_1786 hypothetical protein
* * ÷ CP000730 1932704 1932723 20 2 [1] [1] 2 USA300HOU_1798 hypothetical protein
* * ÷ CP000730 1933212 1933433 222 2 [1] [1] 2 USA300HOU_1798 hypothetical protein
* * ÷ CP000730 1934682 1935483 802 2 [1] [1] 2 [USA300HOU_1798] [USA300HOU_1798]
* * ÷ CP000730 1945281 1945323 43 2 [1] [0] 3 splA/USA300HOU_1807 S1B family serine protease SplA/hypothetical protein
* * ÷ CP000730 1955106 1955221 116 2 [1] [1] 2 [USA300HOU_1816] [USA300HOU_1816]
* * ÷ CP000730 1958454 1958753 300 2 [1] [1] 2 lukE/USA300HOU_1819 leukotoxin LukE/hypothetical protein
* * ÷ CP000730 1971985 1972112 128 2 [1] [1] 2 [USA300HOU_1832] [USA300HOU_1832]
* * ÷ CP000730 1994024 1994221 198 2 [1] [1] 2 USA300HOU_1854/USA300HOU_1855 hypothetical protein/IS1181 transposase
* * ÷ CP000730 1995662 1995727 66 3 [1] [1] 2 USA300HOU_1855 IS1181 transposase
* * ÷ CP000730 2003558 2003656 99 2 [1] [1] 2 rrs3/perR 16S ribosomal RNA/Fur family transcriptional regulator
* * ÷ CP000730 2003971 2004011 41 2 [1] [1] 2 rrs3/perR 16S ribosomal RNA/Fur family transcriptional regulator
* * ÷ CP000730 2019104 2019140 37 2 [1] [1] 2 mgt/yraA transglycosylase/C56 family endopeptidase PfpI
* * ÷ CP000730 2024801 2024902 102 2 [1] [1] 2 USA300HOU_1878/yihY hypothetical protein/possible ribonuclease BN
* * ÷ CP000730 2055518 2055725 208 2 [1] [1] 2 [sspP] [sspP]
* * ÷ CP000730 2072586 2072629 44 2 [1] [1] 2 USA300HOU_1927/USA300HOU_1928 hypothetical protein/C45 family peptidase
* * ÷ CP000730 2080502 2080555 54 2 [1] [1] 2 [USA300HOU_1938] [USA300HOU_1938]
* * ÷ CP000730 2085530 2085751 222 2 [1] [1] 2 [USA300HOU_1944] [USA300HOU_1944]
* * ÷ CP000730 2087105 2087472 368 2 [1] [1] 2 USA300HOU_1946/chp hypothetical protein/chemotaxis inhibitory protein CHIPS
* * ÷ CP000730 2135333 2135498 166 2 [1] [1] 2 [tcmP] [tcmP]
* * ÷ CP000730 2181815 2182005 191 2 [1] [1] 2 USA300HOU_t0054/sprL tRNA‑Leu/hypothetical protein
* * ÷ CP000730 2187005 2187091 87 2 [1] [1] 2 [rsbU] [rsbU]
* * ÷ CP000730 2257628 2257806 179 2 [1] [1] 2 yuxK/USA300HOU_2130 hypothetical protein/hypothetical protein
* * ÷ CP000730 2266663 2266869 207 2 [1] [1] 3 USA300HOU_2140 SAP domain protein
* * ÷ CP000730 2335190 2335269 80 2 [1] [1] 2 npdA/USA300HOU_2192 Sir2 family NAD‑dependent deacetylase/hypothetical protein
* * ÷ CP000730 2335458 2335542 85 2 [1] [1] 2 npdA/USA300HOU_2192 Sir2 family NAD‑dependent deacetylase/hypothetical protein
* * ÷ CP000730 2347760 2347848 89 2 [1] [1] 3 USA300HOU_2204 hypothetical protein
* * ÷ CP000730 2348202 2348389 188 2 [1] [1] 2 USA300HOU_2204 hypothetical protein
* * ÷ CP000730 2411329 2411560 232 2 [0] [1] 2 sarR/USA300HOU_2277 staphylococcal accessory regulator A/hypothetical protein
* * ÷ CP000730 2453023 2453180 158 2 [1] [1] 2 fosB/hutG fosfomycin resistance protein/formimidoylglutamase
* * ÷ CP000730 2473374 2473438 65 2 [1] [1] 2 [tcaB] [tcaB]
* * ÷ CP000730 2506985 2507091 107 2 [1] [1] 2 USA300HOU_2367/sarZ hypothetical protein/transcriptional regulator
* * ÷ CP000730 2527580 2527676 97 2 [1] [1] 2 USA300HOU_2385/adcA FNT family formate‑nitrite transporter/ABC superfamily ATP binding cassette transporter, binding protein
* * ÷ CP000730 2543494 2543538 45 2 [0] [1] 2 USA300HOU_2403/hlgC hypothetical protein/gamma hemolysin component C
* * ÷ CP000730 2614662 2614882 221 2 [1] [1] 2 [USA300HOU_2478]–USA300HOU_2479 [USA300HOU_2478],USA300HOU_2479
* * ÷ CP000730 2626730 2626762 33 2 [1] [1] 2 sarT staphylococcal accessory regulator T
* * ÷ CP000730 2627273 2627369 97 3 [1] [0] 2 sarT/sarU staphylococcal accessory regulator T/staphylococcal accessory regulator U
* * ÷ CP000730 2636047 2636218 172 2 [1] [1] 2 fnbA/gntP fibronectin‑binding protein A/GntP family gluconate:proton (H+) symporter
* * ÷ CP000730 2662561 2662641 81 2 [1] [1] 2 [USA300HOU_2515]–[USA300HOU_2516] [USA300HOU_2515],[USA300HOU_2516]
* * ÷ CP000730 2668456 2668510 55 2 [1] [1] 2 USA300HOU_2523/yicL transcriptional regulator/DMT superfamily drug/metabolite transporter
* * ÷ CP000730 2680849 2681125 277 2 [1] [1] 2 [USA300HOU_2538] [USA300HOU_2538]
* * ÷ CP000730 2764275 2764292 18 2 [1] [1] 2 cysJ/gpxA2 sulfite reductase (NADPH) alpha subunit/glutathione peroxidase
* * ÷ CP000730 2766270 2766348 79 2 [1] [1] 2 USA300HOU_2620/USA300HOU_2621 hypothetical protein/ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 2785958 2785970 13 2 [1] [0] 2 aur/isaB M04 family aureolysin/immunodominant antigen B
* * ÷ CP000730 2818490 2818761 272 2 [1] [1] 2 sasA/USA300HOU_2655 serine‑threonine rich protein/hypothetical protein
* * ÷ CP000730 2825295 2825359 65 2 [1] [1] 2 capA/icaR capsular polysaccharide biosynthesis protein CapA/Ica operon transcriptional regulator R

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =7 (0.240)10 (0.460)
+40 bp
9/218 0.6 66.1% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 1998278 = NA (NA)intergenic (‑6/+5) USA300HOU_t0050/rrf4 tRNA‑Val/5S ribosomal RNA
* ? CP000730 = 513613NA (NA)50 (2.740)
+57 bp
28/184 0.1 NA noncoding (821/1540 nt) rrs1 16S ribosomal RNA
?CP000730 513672 = NA (NA)noncoding (880/1540 nt) rrs1 16S ribosomal RNA
* ? CP000730 514102 =NA (NA)3 (0.110) 3/284 1.3 NA noncoding (1310/1540 nt) rrs1 16S ribosomal RNA
?CP000730 514124 = NA (NA)noncoding (1332/1540 nt) rrs1 16S ribosomal RNA
* ? CP000730 2537754 =10 (0.340)3 (0.110) 3/276 1.3 20.5% intergenic (+108/+46) USA300HOU_2397/gpmA2 hypothetical protein/phosphoglycerate mutase
?CP000730 2537797 = 14 (0.510)intergenic (+151/+3) USA300HOU_2397/gpmA2 hypothetical protein/phosphoglycerate mutase