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 39,246 C→T 50.4% A630T (GCT→ACT)  mecA ← penicillin binding protein 2 prime
RA 39,378 C→A 50.2% D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime
RA 110,660 T→A 17.1% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 111,512 A→G 37.0% S194S (TCA→TCG USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,516 C→A 33.4% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 129,029 A→G 8.7% L199L (TTA→CTA)  spa ← immunoglobulin G binding protein A
RA 160,585 A→G 7.0% M260V (ATG→GTG)  deoB1 → phosphopentomutase
RA 225,710 C→G 43.8% T266R (ACA→AGA)  murQ → possible sugar phosphate isomerase
RA 367,644 G→T 100% intergenic (‑96/‑20) nanA ← / → nagC N‑acetylneuraminate lyase/possible transcriptional regulator
RA 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein
RA 496,458 C→A 17.0% S220I (AGC→ATC)  gltC ← glutamate synthase operon transcriptional regulator
RA 512,643 A→G 61.0% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 638,614 G→T 100% T14K (ACA→AAA)  thiD ← phosphomethylpyrimidine kinase
RA 707,879 A→T 100% L11I (TTA→ATA)  mntB ← ABC superfamily ATP binding cassette transporter, ABC protein
RA 790,778 G→A 100% intergenic (+277/‑197) kipA → / → ltaS possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
RA 849,263 C→A 34.2% A130E (GCA→GAA)  yvcJ → ATP‑binding protein
RA 852,632 C→T 18.9% A76V (GCG→GTG)  clpP → S14 family endopeptidase ClpP
RA 880,093 G→T 63.1% intergenic (+271/‑70) USA300HOU_0822 → / → nuc hypothetical protein/micrococcal nuclease
RA 1,064,082 G→T 15.4% A136E (GCA→GAA)  brpA ← LytR family transcriptional regulator
RA 1,103,408 A→G 10.8% L310L (TTA→TTG pdhA → pyruvate dehydrogenase (acetyl‑transferring) alpha subunit
RA 1,232,465 G→C 100% A124P (GCG→CCG)  prkC → non‑specific serine/threonine protein kinase
RA 1,233,332 C→A 39.5% P413T (CCT→ACT)  prkC → non‑specific serine/threonine protein kinase
RA 1,416,458 A→T 100% I216N (ATT→AAT)  oppD ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,440,007 Δ1 bp 100% coding (34/201 nt) cspA ← cold shock protein CspA
RA 1,474,639 C→G 100% A9129P (GCA→CCA)  ebh ← extracellular matrix binding protein
RA 1,481,355 G→T 100% A6890E (GCA→GAA)  ebh ← extracellular matrix binding protein
RA 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_1379 → hypothetical membrane protein
RA 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,454 C→T 100% G73D (GGC→GAC)  apt ← adenine phosphoribosyltransferase
RA 1,775,439 C→T 49.7% G362D (GGT→GAT)  clpX ← S14 family endopeptidase ClpX
RA 1,797,772 G→C 100% R7G (CGC→GGC)  phoR ← sensor histidine kinase
RA 1,944,670 G→A 12.8% intergenic (‑251/‑713) splA ← / → USA300HOU_1807 S1B family serine protease SplA/hypothetical protein
RA 1,989,071 C→T 10.5% G17S (GGT→AGT)  cspR ← TrmH family RNA methyltransferase
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,013,179 A→T 28.0% Q19H (CAA→CAT yfhP → possible metal‑dependent hydrolase
RA 2,026,655 C→T 12.9% E87K (GAA→AAA)  vraR ← response regulator VraR
RA 2,028,542 G→C 22.2% L35V (CTC→GTC)  yvqF ← hypothetical membrane protein
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,532,298 A→T 100% T15T (ACA→ACT murN → FemAB family peptidoglycan biosynthesis protein
RA 2,727,823 C→T 8.5% intergenic (‑42/‑176) USA300HOU_2582 ← / → pyrD hypothetical protein/dihydroorotate oxidase
RA 2,775,041 A→G 12.2% D715D (GAT→GAC clfB ← clumping factor B
RA 2,803,971 A→T 15.4% V718D (GTC→GAC)  secA2 ← Sec family Type I general secretory pathway protein SecA
RA 2,856,087 T→A 100% P80P (CCT→CCA USA300HOU_2698 → hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =33 (0.980)28 (1.200)
+40 bp
25/180 NT 55.2% 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