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

Predicted mutations
evidence position mutation freq annotation gene description
RA 19,348 G→A 16.2% G335D (GGT→GAT)  yybT → DHH subfamily phosphodiesterase
RA 39,378 C→A 100% D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime
RA 76,969 G→A 100% intergenic (+1027/‑107) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 110,651 C→T 12.1% D170D (GAC→GAT USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 110,660 T→A 13.8% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 111,512 A→G 32.2% S194S (TCA→TCG USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,516 C→A 31.2% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,560 T→C 22.0% R210R (CGT→CGC USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,572 C→T 10.2% D214D (GAC→GAT USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 116,951 T→C 7.8% G356G (GGT→GGC amd → M20 family peptidase
RA 178,003 C→A 12.6% intergenic (+1811/‑23) cap5C → / → cap5E capsular polysaccharide biosynthesis protein Cap5C/capsular polysaccharide biosynthesis protein Cap5E
RA 195,286 T→A 100% intergenic (‑97/‑82) USA300HOU_0183 ← / → USA300HOU_0184 hypothetical protein/hypothetical protein
RA 355,466 G→A 100% P412S (CCA→TCA)  brnQ1 ← LIVCS family branched chain amino acid:cation symporter
RA 396,540 G→A 100% A208T (GCA→ACA)  USA300HOU_0364 → possible lipoprotein
RA 512,643 A→G 54.9% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 607,884 G→A 100% R209* (CGA→TGA)  dck ← deoxynucleoside kinase
RA 629,681 C→A 100% L84I (CTA→ATA)  hxlA → possible 3‑hexulose‑6‑phosphate synthase
RA 665,392 T→G 100% L79* (TTA→TGA)  iolS → possible acetytransferase
RA 707,910 A→G 100% intergenic (‑1/‑121) mntB ← / → sirR ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator
RA 861,896 C→T 6.6% N459N (AAC→AAT pgm → bisphosphoglycerate mutase
RA 874,718 A→C 100% K541N (AAA→AAC clfA → fibrinogen‑binding protein
RA 1,064,253 Δ1 bp 100% coding (236/1218 nt) brpA ← LytR family transcriptional regulator
RA 1,233,504 T→A 100% V470D (GTT→GAT)  prkC → non‑specific serine/threonine protein kinase
RA 1,238,026 T→A 9.4% L47H (CTT→CAT)  yloV → glycerone kinase
RA 1,344,530 G→A 7.1% intergenic (+266/‑163) USA300HOU_1253 → / → USA300HOU_1255 hypothetical protein/hypothetical protein
RA 1,392,673 A→G 7.8% intergenic (+447/‑47) alsT → / → glcT AGCS family alanine or glycine:sodium (Na+) symporter/transcriptional antiterminator
RA 1,392,698 C→T 8.1% intergenic (+472/‑22) alsT → / → glcT AGCS family alanine or glycine:sodium (Na+) symporter/transcriptional antiterminator
RA 1,416,458 A→T 100% I216N (ATT→AAT)  oppD ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
RA 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_1379 → hypothetical membrane protein
RA 1,525,990 A→G 7.8% S651S (TCT→TCC dnaQ ← DNA‑directed DNA polymerase III epsilon subunit
RA 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,362 G→A 100% H104Y (CAC→TAC)  apt ← adenine phosphoribosyltransferase
RA 1,761,889 C→A 100% D388Y (GAT→TAT)  folC ← tetrahydrofolate synthase
RA 1,776,114 G→A 29.8% P137L (CCA→CTA)  clpX ← S14 family endopeptidase ClpX
RA 1,963,768 C→G 100% V365L (GTA→CTA)  hemG ← protoporphyrinogen oxidase
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,027,672 C→A 100% G92V (GGC→GTC)  vraS ← sensor histidine kinase VraS
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,352,815 G→A 100% A92V (GCA→GTA)  rpsI ← ribosomal protein S9
RA 2,454,626 A→T 100% L48L (CTA→CTT USA300HOU_2315 → hypothetical membrane protein
RA 2,470,111 G→A 54.9% S575L (TCA→TTA)  semB ← MFS family major facilitator transporter, multidrug:cation symporter
RA 2,532,298 A→T 100% T15T (ACA→ACT murN → FemAB family peptidoglycan biosynthesis protein
RA 2,656,349 C→A 10.5% A53S (GCA→TCA)  USA300HOU_2509 ← possible lactoylglutatione lyase
RA 2,810,588 T→C 10.2% S266G (AGC→GGC)  secY2 ← Sec family Type I general secretory pathway protein SecY
RA 2,836,655 A→G 6.4% Y112H (TAC→CAC)  hisB ← imidazoleglycerol‑phosphate dehydratase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 52495 =41 (0.840)52 (1.070)
+T
3/258 NT 58.3% intergenic (+105/‑568) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
?CP000730 = 52988 34 (0.700)intergenic (+598/‑75) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
* ? CP000730 512620 =40 (0.820)43 (1.280)
+40 bp
32/180 NT 60.9% 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 = 121769345 (0.920)3 (0.070) 3/228 NT 7.1% intergenic (+22/‑415) USA300HOU_1144/USA300HOU_1145 hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase
?CP000730 = 1217729 39 (0.910)intergenic (+58/‑379) USA300HOU_1144/USA300HOU_1145 hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase
* ? CP000730 = 247645347 (0.960)3 (0.070) 3/236 NT 6.3% intergenic (‑198/+42) tcaA/tcaR teicoplanin resistance protein TcaA/transcriptional regulator TcaR
?CP000730 = 2476476 46 (1.040)intergenic (‑221/+19) tcaA/tcaR teicoplanin resistance protein TcaA/transcriptional regulator TcaR
* ? CP000730 = 267142045 (0.920)3 (0.060) 3/250 NT 6.5% coding (171/345 nt) ydfQ possible thioredoxin
?CP000730 = 2671462 43 (0.920)coding (129/345 nt) ydfQ possible thioredoxin