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 39,378 C→A 100% D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime
RA 110,651 C→T 18.3% D170D (GAC→GAT USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 110,660 T→A 16.5% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 111,512 A→G 32.1% S194S (TCA→TCG USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,516 C→A 32.8% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 221,865 C→A 7.4% G475V (GGC→GTC)  glcB ← PTS family glucose/glucoside (glc) porter component IIABC
RA 367,644 G→T 100% intergenic (‑96/‑20) nanA ← / → nagC N‑acetylneuraminate lyase/possible transcriptional regulator
RA 423,247 A→G 100% V112V (GTA→GTG USA300HOU_0394 → hypothetical protein
RA 454,656 G→A 100% V119I (GTT→ATT)  set23 → staphylococcal exotoxin
RA 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein
RA 512,643 A→G 49.3% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 583,939 G→A 6.9% intergenic (+23/‑249) rplA → / → rplJ ribosomal protein L1/ribosomal protein L10
RA 638,614 G→T 100% T14K (ACA→AAA)  thiD ← phosphomethylpyrimidine kinase
RA 693,258 T→A 8.3% I65F (ATT→TTT)  USA300HOU_0636 ← hypothetical protein
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 911,610 G→A 100% intergenic (‑221/‑107) USA300HOU_0869 ← / → sufC hypothetical membrane protein/ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,199,222 C→A 10.7% F80L (TTC→TTA ylmG → hypothetical protein
RA 1,232,465 G→C 100% A124P (GCG→CCG)  prkC → non‑specific serine/threonine protein kinase
MC JC 1,302,967 Δ4 bp 100% coding (325‑328/714 nt) USA300HOU_1209 → possible GntR family transcriptional regulator
RA 1,416,458 A→T 100% I216N (ATT→AAT)  oppD ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,419,527 G→T 100% P7T (CCT→ACT)  USA300HOU_1317 ← hypothetical membrane 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 1,551,783 A→G 7.4% S231P (TCA→CCA)  ebpS ← elastin‑binding protein
RA 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,672,434 C→T 72.4% A187T (GCA→ACA)  rpoD ← DNA‑directed RNA polymerase sigma subunit RpoD
RA 1,744,454 C→T 100% G73D (GGC→GAC)  apt ← adenine phosphoribosyltransferase
RA 1,784,962 C→T 5.0% G40D (GGC→GAC)  thrS ← threonine‑‑tRNA ligase
RA 1,797,772 G→C 100% R7G (CGC→GGC)  phoR ← sensor histidine kinase
RA 1,802,628 A→T 7.8% K321M (AAG→ATG)  cycA → APC family amino acid‑polyamine‑organocation transporter
RA 1,809,898 A→G 6.5% F91F (TTT→TTC accD ← acetyl‑CoA carboxylase beta subunit
RA 1,944,670 G→A 100% intergenic (‑251/‑713) splA ← / → USA300HOU_1807 S1B family serine protease SplA/hypothetical protein
RA 1,946,057 G→A 8.9% intergenic (+108/+366) USA300HOU_1807 → / ← epiG hypothetical protein/lantibiotic epidermin immunity protein F
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,026,655 C→T 100% E87K (GAA→AAA)  vraR ← response regulator VraR
RA 2,261,772 T→C 5.6% V185V (GTA→GTG USA300HOU_2133 ← hypothetical protein
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,289,325 C→A 100% Q55H (CAG→CAT ybbP ← hypothetical membrane protein
RA 2,386,119 G→A 62.5% P114L (CCG→CTG)  USA300HOU_2245 ← hypothetical protein
RA 2,502,141 C→A 100% A222D (GCC→GAC)  USA300HOU_2364 → AraC transcriptional regulator
RA 2,532,298 A→T 100% T15T (ACA→ACT murN → FemAB family peptidoglycan biosynthesis protein
RA 2,679,455 Δ1 bp 100% intergenic (+327/‑62) USA300HOU_2535 → / → cbpD hypothetical protein/possible secretory antigen
RA 2,710,893 Δ1 bp 100% coding (34/1812 nt) oatA ← possible acetyltransferase
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 34173 =72 (1.140)5 (0.080) 5/246 NT 7.0% coding (462/480 nt) orfX hypothetical protein OrfX
?CP000730 = 57858 64 (1.070)intergenic (+304/+613) USA300HOU_0048/USA300HOU_0049 hypothetical membrane protein/hypothetical protein
* ? CP000730 52495 =62 (0.990)111 (1.780)
+T
3/256 NT 63.3% intergenic (+105/‑568) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
?CP000730 = 52988 68 (1.080)intergenic (+598/‑75) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
* ? CP000730 512620 =84 (1.330)47 (1.090)
+40 bp
34/178 NT 44.9% 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 2001491 =11 (0.170)3 (0.050) 3/244 NT 22.4% intergenic (‑100/+116) rrl3/USA300HOU_t0051 23S ribosomal RNA/tRNA‑Ala
?CP000730 2179606 = NA (NA)intergenic (‑50/+262) rrl4/rrs4 23S ribosomal RNA/16S ribosomal RNA
* ? CP000730 = 267454269 (1.100)6 (0.100) 3/238 NT 8.2% intergenic (‑21/+247) ptsG/ilvB2 PTS family glucose/glucoside (glc) porter component IIABC/pyruvate oxidase
?CP000730 = 2674577 71 (1.220)intergenic (‑56/+212) ptsG/ilvB2 PTS family glucose/glucoside (glc) porter component IIABC/pyruvate oxidase
* ? CP000730 = 277774541 (0.650)3 (0.050) 3/244 NT 6.9% coding (495/705 nt) arcR transcriptional regulator
?CP000730 = 2777785 42 (0.710)coding (455/705 nt) arcR transcriptional regulator