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

Predicted mutations
evidence seq id position mutation freq annotation gene description
RA CP000731 81 N→G 100% intergenic (–/‑151)  / → repA –/replication protein A
JC CP000731 6,552 +28 bp 100% intergenic (+1069/‑419) cadX → / → USA300HOU_pUSA300HOUMR0010 cadmium efflux regulator/MarR family transcriptional regulator
RA CP000731 15,413 C→T 13.8% D68N (GAC→AAC)  USA300HOU_pUSA300HOUMR0019 ← strepthothricin acetyltransferase
RA CP000731 25,663 Δ1 bp 100% coding (316/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein
RA USA300TCH1516_ALE 110,651 C→T 14.0% D170D (GAC→GAT USA300HOU_RS00515 → putative lipoprotein
RA USA300TCH1516_ALE 110,660 T→A 21.2% I173I (ATT→ATA USA300HOU_RS00515 → putative lipoprotein
RA USA300TCH1516_ALE 111,512 A→G 31.5% S194S (TCA→TCG USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 111,516 C→A 30.7% Q196K (CAA→AAA)  USA300HOU_RS00520 → putative lipoprotein
RA USA300TCH1516_ALE 111,560 T→C 11.3% R210R (CGT→CGC USA300HOU_RS00520 → putative lipoprotein
JC USA300TCH1516_ALE 130,854 (T)5→1 14.4% intergenic (‑94/+272) sarS ← / ← yfhA HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA
RA USA300TCH1516_ALE 512,643 A→G 54.5% intergenic (+711/‑6052) recR → / → speA_2 Recombination protein RecR/Arginine decarboxylase
RA USA300TCH1516_ALE 590,688 G→A 5.4% G302S (GGT→AGT)  rpoC → DNA‑directed RNA polymerase subunit beta'
RA USA300TCH1516_ALE 622,533 T→C 17.4% D1032D (GAT→GAC sdrE → Serine‑aspartate repeat‑containing protein E
RA USA300TCH1516_ALE 849,017 C→T 17.5% P48L (CCT→CTT)  USA300HOU_RS04145 → Nucleotide‑binding protein
RA USA300TCH1516_ALE 1,097,015 T→C 7.4% M270T (ATG→ACG)  ythB → Putative cytochrome bd menaquinol oxidase subunit II
RA USA300TCH1516_ALE 1,416,458 A→T 100% I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD
RA USA300TCH1516_ALE 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_RS07375 → hypothetical protein
RA USA300TCH1516_ALE 1,646,189 G→C 100% A155G (GCA→GGA)  ypdF ← Aminopeptidase YpdF
RA USA300TCH1516_ALE 1,892,051 A→T 20.9% intergenic (‑144/+376) rot ← / ← USA300TCH1516_01749 HTH‑type transcriptional regulator rot/hypothetical protein
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,028,508 A→T 22.2% V46E (GTA→GAA)  USA300HOU_RS10230 ← hypothetical protein
RA USA300TCH1516_ALE 2,154,656 A→G 6.2% F341L (TTT→CTT)  nrgA ← Ammonium transporter NrgA
RA USA300TCH1516_ALE 2,211,305 A→G 24.9% intergenic (+298/+515) USA300HOU_RS11275 → / ← yidC hypothetical protein/Membrane protein insertase YidC
RA USA300TCH1516_ALE 2,279,705 G→A 100% A943V (GCA→GTA)  ebh_3 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 2,328,291 G→A 6.4% A458V (GCA→GTA)  lacE ← PTS system lactose‑specific EIICB component
RA USA300TCH1516_ALE 2,372,586 G→T 19.5% S397* (TCA→TAA)  pbuG ← Guanine/hypoxanthine permease PbuG
RA USA300TCH1516_ALE 2,373,715 C→A 9.8% G21C (GGT→TGT)  pbuG ← Guanine/hypoxanthine permease PbuG
RA USA300TCH1516_ALE 2,373,809 A→T 15.4% intergenic (‑34/+79) pbuG ← / ← topB Guanine/hypoxanthine permease PbuG/DNA topoisomerase 3
RA USA300TCH1516_ALE 2,504,989 T→C 10.3% intergenic (+293/+111) USA300HOU_RS12890 → / ← gltT hypothetical protein/Proton/sodium‑glutamate symport protein
RA USA300TCH1516_ALE 2,532,298 A→T 100% T15T (ACA→ACT femA_3 → Aminoacyltransferase FemA
RA USA300TCH1516_ALE 2,726,142 A→G 6.3% Y48H (TAT→CAT)  USA300HOU_RS14025 ← hypothetical protein
RA USA300TCH1516_ALE 2,755,876 C→T 5.4% A202T (GCG→ACG)  opuD_3 ← Glycine betaine transporter OpuD
RA USA300TCH1516_ALE 2,774,993 A→G 14.4% D731D (GAT→GAC clfB ← Clumping factor B
RA USA300TCH1516_ALE 2,775,041 A→G 13.3% D715D (GAT→GAC clfB ← Clumping factor B
RA USA300TCH1516_ALE 2,860,200 C→T 5.5% R211C (CGT→TGT)  bceA_2 → Bacitracin export ATP‑binding protein BceA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =54 (0.960)40 (1.030)
+40 bp
28/178 NT 51.9% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE 1998278 = NA (NA)intergenic (‑6/+3329) USA300TCH1516_01882/USA300TCH1516_01883 tRNA‑Val/tRNA‑Ala