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 26,506 C→G R281G (CGC→GGC)  vicK → sensor histidine kinase VicK
RA 36,378 C→T L58L (TTG→TTA)  tpn ← IS431mec transposase
RA 603,961 G→A M465I (ATG→ATA)  araB → ribulokinase
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 1,646,189 G→C A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,446 G→A P76S (CCT→TCT)  apt ← adenine phosphoribosyltransferase
RA 1,899,742 A→G N421N (AAT→AAC)  USA300HOU_1761 ← hypothetical protein
RA 2,010,363 C→T C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,030,815 G→T A90S (GCA→TCA)  USA300HOU_1885 → hypothetical membrane protein
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
RA 2,722,719 C→T G13D (GGT→GAT)  cobW3 ← cobalamin (vitamin B12) biosynthesis protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP000730 45614 45658 45 2 [1] [1] 2 USA300HOU_0038/ccrB hypothetical protein/cassette chromosome recombinase B
* * ÷ CP000730 54593 54624 32 2 [0] [1] 3 USA300HOU_0044/cch possible transcriptional regulator/possible beta‑lactamase
* * ÷ CP000730 58290 58444 155 2 [1] [1] 2 USA300HOU_0048/USA300HOU_0049 hypothetical membrane protein/hypothetical protein
* * ÷ CP000730 58692 58927 236 2 [1] [1] 2 USA300HOU_0049/USA300HOU_0050 hypothetical protein/hypothetical protein
* * ÷ CP000730 60702 60780 79 2 [1] [0] 2 [USA300HOU_0052] [USA300HOU_0052]
* * ÷ CP000730 63793 63879 87 2 [1] [1] 2 [USA300HOU_0058] [USA300HOU_0058]
* * ÷ CP000730 70775 70894 120 4 [1] [1] 2 [arcB1]–[arcR] [arcB1],[arcR]
* * ÷ CP000730 85071 85121 51 2 [1] [0] 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 129660 129783 124 2 [1] [1] 3 spa/sarH1 immunoglobulin G binding protein A/staphylococcal accessory regulator H1
* * ÷ CP000730 153956 154081 126 2 [1] [1] 2 USA300HOU_0144/sodM MOP superfamily multidrug/oligosaccharidyl‑lipid/polysaccharide flippase transporter/superoxide dismutase
* * ÷ CP000730 169458 169644 187 2 [1] [0] 2 [USA300HOU_0160] [USA300HOU_0160]
* * ÷ CP000730 169697 169751 55 2 [0] [1] 2 USA300HOU_0160 hypothetical protein
* * ÷ CP000730 346091 346160 70 2 [1] [1] 2 USA300HOU_0310/USA300HOU_0311 hypothetical membrane protein/hypothetical protein
* * ÷ CP000730 352812 352862 51 3 [1] [0] 2 USA300HOU_0321/USA300HOU_0322 hypothetical protein/hypothetical protein
* * ÷ CP000730 471137 471219 83 2 [1] [1] 2 USA300HOU_0446/USA300HOU_0447 hypothetical lipoprotein/hypothetical lipoprotein
* * ÷ CP000730 604323 604345 23 2 [1] [1] 2 araB/USA300HOU_0546 ribulokinase/possible UDP‑glucose 4‑epimerase
* * ÷ CP000730 679481 679576 96 2 [1] [1] 2 sarA/USA300HOU_0623 staphylococcal accessory regulator A/hypothetical protein
* * ÷ CP000730 745439 745504 66 2 [0] [1] 2 sarX possible staphylococcal accessory protein X
* * ÷ CP000730 790811 790854 44 3 [1] [1] 2 kipA/ltaS possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
* * ÷ CP000730 880008 880141 134 2 [1] [1] 2 USA300HOU_0822/nuc hypothetical protein/micrococcal nuclease
* * ÷ CP000730 918138 918219 82 2 [1] [1] 2 USA300HOU_0877/USA300HOU_0878 hypothetical membrane protein/CBS domain protein
* * ÷ CP000730 974400 974510 111 2 [1] [1] 2 yitW/oatA hypothetical protein/acyltransferase
* * ÷ CP000730 979606 979688 83 2 [1] [1] 2 USA300HOU_0934 LysR family transcriptional regulator
* * ÷ CP000730 980380 980440 61 3 [1] [1] 2 leuA1 2‑isopropylmalate synthase
* * ÷ CP000730 982871 982984 114 2 [1] [1] 2 USA300HOU_0938 hypothetical membrane protein
* * ÷ CP000730 983170 983223 54 2 [0] [1] 2 USA300HOU_0938 hypothetical membrane protein
* * ÷ CP000730 987991 988061 71 2 [0] [0] 2 USA300HOU_0943/oppB1 hypothetical membrane protein/oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 988097 988145 49 2 [0] [1] 2 oppB1 oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 1016372 1016448 77 2 [0] [1] 3 USA300HOU_0970/USA300HOU_0971 hypothetical membrane protein/AGCS family alanine or glycine:sodium (Na+) or proton (H+) symporter
* * ÷ CP000730 1018994 1019039 46 3 [1] [1] 2 USA300HOU_0972/yjcG possible esterase/2'‑5' RNA ligase
* * ÷ CP000730 1033691 1033712 22 2 [0] [1] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1040830 1040993 164 3 [1] [0] 2 USA300HOU_0983/USA300HOU_0984 competence protein/glycosyltransferase
* * ÷ CP000730 1054549 1054656 108 2 [1] [1] 2 sspA/atl S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase
* * ÷ CP000730 1166068 1166356 289 2 [1] [0] 2 USA300HOU_1092/USA300HOU_1093 hypothetical protein/hypothetical membrane protein
* * ÷ CP000730 1167011 1167048 38 2 [0] [1] 2 USA300HOU_1093/USA300HOU_1094 hypothetical membrane protein/fibrinogen‑binding protein
* * ÷ CP000730 1171648 1171984 337 2 [0] [1] 3 [USA300HOU_1100] [USA300HOU_1100]
* * ÷ CP000730 1339383 1339535 153 2 [1] [1] 2 [USA300HOU_1242] [USA300HOU_1242]
* * ÷ CP000730 1339830 1339929 100 2 [1] [1] 2 USA300HOU_1242/USA300HOU_1243 hypothetical protein/hypothetical protein
* * ÷ CP000730 1343297 1343416 120 2 [0] [1] 2 [USA300HOU_1250] [USA300HOU_1250]
* * ÷ CP000730 1349523 1349556 34 2 [0] [1] 2 [yvfR] [yvfR]
* * ÷ CP000730 1415506 1415591 86 2 [1] [1] 2 [USA300HOU_1312] [USA300HOU_1312]
* * ÷ CP000730 1439452 1439603 152 2 [1] [1] 3 USA300HOU_1336 hypothetical membrane protein
* * ÷ CP000730 1449343 1449381 39 2 [1] [1] 2 USA300HOU_1346/odhB hypothetical protein/dihydrolipoyllysine‑residue succinyltransferase
* * ÷ CP000730 1456642 1456669 28 2 [1] [0] 2 USA300HOU_1351/USA300HOU_1352 hypothetical protein/hypothetical protein
* * ÷ CP000730 1457342–1457731 1457774 44–433 2 [1] [1] 2 [arlR]–[USA300HOU_1354] [arlR],[USA300HOU_1354]
* * ÷ CP000730 1507652 1507753 102 2 [1] [0] 2 ald1/polA alanine dehydrogenase/5'‑3' exonuclease
* * ÷ CP000730 1523575 1523622 48 2 [1] [1] 2 dnaD1/asnS DNA replication protein DnaD/asparagine‑‑tRNA ligase
* * ÷ CP000730 1539327 1539468 142 2 [1] [1] 2 USA300HOU_1405 hypothetical protein
* * ÷ CP000730 1562003 1562302 300 2 [1] [1] 2 [lukS‑PV] [lukS‑PV]
* * ÷ CP000730 1608885 1608967 83 2 [0] [0] 2 USA300HOU_1492/srrB possible lipoprotein/sensor histidine kinase SrrB
* * ÷ CP000730 1697748 1697774 27 2 [1] [1] 2 rpsT/holA ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit
* * ÷ CP000730 1709706 1709764 59 2 [0] [1] 2 sem/USA300HOU_1604 enterotoxin/hypothetical protein
* * ÷ CP000730 1747091 1747119 29 2 [1] [1] 2 USA300HOU_1635/secDF hypothetical protein/RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter
* * ÷ CP000730 1749626 1749674 49 2 [1] [1] 2 secDF/yajC RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter/Sec family Type I general secretory pathway preprotein translocase subunit YajC
* * ÷ CP000730 1928105 1928208 104 2 [0] [0] 2 [USA300HOU_1792] [USA300HOU_1792]
* * ÷ CP000730 1939450 1939478 29 3 [1] [1] 2 hsdM2/splF type I site‑specific deoxyribonuclease methyltransferase subunit/S1B family serine protease SplF
* * ÷ CP000730 1958651 1958724 74 2 [0] [1] 2 lukE/USA300HOU_1819 leukotoxin LukE/hypothetical protein
* * ÷ CP000730 2003587 2003635 49 2 [1] [1] 3 rrs3/perR 16S ribosomal RNA/Fur family transcriptional regulator
* * ÷ CP000730 2015196 2015220 25 2 [1] [1] 2 [USA300HOU_1865]–[rgpD] [USA300HOU_1865],[rgpD]
* * ÷ CP000730 2019112 2019156 45 2 [1] [1] 2 mgt/yraA transglycosylase/C56 family endopeptidase PfpI
* * ÷ CP000730 2055652 2055736 85 3 [1] [1] 2 [sspP] [sspP]
* * ÷ CP000730 2085408 2085517 110 2 [1] [1] 2 mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
* * ÷ CP000730 2086136 2086138 3 2 [0] [0] 2 USA300HOU_1945/USA300HOU_1946 hypothetical protein/hypothetical protein
* * ÷ CP000730 2086352 2086417 66 2 [1] [1] 2 USA300HOU_1945/USA300HOU_1946 hypothetical protein/hypothetical protein
* * ÷ CP000730 2087278 2087518 241 2 [1] [1] 2 USA300HOU_1946/chp hypothetical protein/chemotaxis inhibitory protein CHIPS
* * ÷ CP000730 2089643 2089707 65 2 [1] [1] 2 USA300HOU_1950/ami hypothetical protein/N‑acetylmuramoyl‑L‑alanine amidase
* * ÷ CP000730 2126925 2127063 139 4 [1] [1] 2 [USA300HOU_2008] [USA300HOU_2008]
* * ÷ CP000730 2131573 2131721 149 3 [1] [0] 2 USA300HOU_2013/dapE possible leukocidin subunit/M20A family peptidase
* * ÷ CP000730 2134416 2134493 78 2 [1] [1] 2 [tcmP] [tcmP]
* * ÷ CP000730 2135402 2135418 17 2 [1] [0] 2 tcmP/USA300HOU_2018 ferrichrome ABC superfamily ATP binding cassette transporter, binding protein/Trk family potassium (K+) transporter, ABC protein
* * ÷ CP000730 2135456 2135518 63 2 [0] [1] 2 [USA300HOU_2018] [USA300HOU_2018]
* * ÷ CP000730 2181732 2181922 191 3 [1] [1] 3 USA300HOU_t0054/sprL tRNA‑Leu/hypothetical protein
* * ÷ CP000730 2257546 2257596 51 2 [1] [0] 2 yuxK/USA300HOU_2130 hypothetical protein/hypothetical protein
* * ÷ CP000730 2335267 2335535 269 2 [1] [0] 2 npdA/USA300HOU_2192 Sir2 family NAD‑dependent deacetylase/hypothetical protein
* * ÷ CP000730 2348344 2348423 80 2 [1] [1] 3 USA300HOU_2204 hypothetical protein
* * ÷ CP000730 2348638 2348840 203 3 [1] [0] 2 [USA300HOU_2204]–[clpA] [USA300HOU_2204],[clpA]
* * ÷ CP000730 2348919 2348949 31 2 [0] [0] 2 clpA S14 family endopeptidase ClpA
* * ÷ CP000730 2435059 2435162 104 2 [1] [1] 2 [yifK] [yifK]
* * ÷ CP000730 2436743 2436768 26 2 [1] [0] 2 yifK/USA300HOU_2300 APC family amino acid‑polyamine‑organocation transporter/hypothetical membrane protein
* * ÷ CP000730 2455741 2455766 26 2 [1] [1] 2 [USA300HOU_2315] [USA300HOU_2315]
* * ÷ CP000730 2543426 2543436 11 2 [0] [1] 2 USA300HOU_2403/hlgC hypothetical protein/gamma hemolysin component C
* * ÷ CP000730 2627253 2627336 84 2 [1] [1] 2 sarT/sarU staphylococcal accessory regulator T/staphylococcal accessory regulator U
* * ÷ CP000730 2660551 2660590 40 2 [1] [1] 2 [ddh] [ddh]
* * ÷ CP000730 2680610 2680800 191 2 [1] [1] 2 [USA300HOU_2537]–[USA300HOU_2538] [USA300HOU_2537],[USA300HOU_2538]
* * ÷ CP000730 2761003 2761104 102 2 [1] [1] 2 citM/USA300HOU_2616 CitMHS family citrate‑magnesium (Mg2+):proton (H+) citrate‑calcium (Ca2+):proton (H+) symporter/hypothetical protein
* * ÷ CP000730 2797772 2797830 59 3 [1] [1] 2 acmB/USA300HOU_2645 possible N‑acetylmuramoyl‑L‑alanine amidase/possible isochorismatase hydrolase
* * ÷ CP000730 2825261 2825401 141 5 [1] [1] 3 capA/icaR capsular polysaccharide biosynthesis protein CapA/Ica operon transcriptional regulator R
* * ÷ CP000730 2825621 2825623 3 2 [0] [0] 2 capA/icaR capsular polysaccharide biosynthesis protein CapA/Ica operon transcriptional regulator R
* * ÷ CP000730 2825841 2825850 10 2 [0] [0] 2 capA/icaR capsular polysaccharide biosynthesis protein CapA/Ica operon transcriptional regulator R
* * ÷ CP000730 2859352 2859363 12 2 [0] [1] 2 USA300HOU_2702/vraD hypothetical membrane protein/ABC superfamily ATP binding cassette transporter, ABC protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =10 (0.420)12 (0.720)
+40 bp		 12/188 0.4 63.1% 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 513989 =NA (NA)3 (0.130) 3/252 1.8 NA noncoding (1197/1540 nt) rrs1 16S ribosomal RNA
?CP000730 514015 = NA (NA)noncoding (1223/1540 nt) rrs1 16S ribosomal RNA