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 30,243 A→G 5.9% V583V (GTA→GTG carB → carbamoyl‑phosphate synthase large subunit
RA 30,250 T→G 6.0% S586A (TCG→GCG)  carB → carbamoyl‑phosphate synthase large subunit
RA 30,273 T→C 6.5% G593G (GGT→GGC carB → carbamoyl‑phosphate synthase large subunit
RA 138,668 G→A 7.0% S500L (TCA→TTA)  htrE ← predicted outer membrane usher protein
RA 138,670 G→T 6.3% Y499* (TAC→TAA htrE ← predicted outer membrane usher protein
RA 138,673 A→C 6.4% N498K (AAT→AAG) ‡ htrE ← predicted outer membrane usher protein
RA 138,675 T→C 6.0% N498D (AAT→GAT) ‡ htrE ← predicted outer membrane usher protein
RA 204,511 C→T 100% intergenic (+111/‑73) alaV → / → rrlH tRNA‑Ala/23S ribosomal RNA
RA 204,556 A→G 100% intergenic (+156/‑28) alaV → / → rrlH tRNA‑Ala/23S ribosomal RNA
RA 214,925 A→C 33.4% D12A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 214,931 A→C 33.5% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit
RA 1,036,505 G→A 100% A632A (GCG→GCA rsxC → fused predicted 4Fe‑4S ferredoxin‑type protein
RA 1,221,878 A→G 5.9% Q151Q (CAA→CAG yebT → conserved hypothetical protein
RA 1,221,883 A→T 6.0% K153I (AAA→ATA)  yebT → conserved hypothetical protein
RA 1,221,886 A→T 6.4% Y154F (TAT→TTT)  yebT → conserved hypothetical protein
RA 1,221,891 C→T 6.1% L156L (CTG→TTG)  yebT → conserved hypothetical protein
RA 1,318,494 C→A 8.1% R29L (CGT→CTT)  cld ← regulator of length of O‑antigen component of lipopolysaccharide chains
RA 1,763,556 T→C 43.8% noncoding (288/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,558 G→C 8.4% noncoding (286/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,636 A→G 33.3% noncoding (208/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,804,090 G→A 26.8% G52G (GGG→GGA mprA → DNA‑binding transcriptional regulator
RA 1,826,740 G→T 7.6% intergenic (‑417/‑18) hydN ← / → mutS formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein
RA 1,826,741 G→A 7.7% intergenic (‑418/‑17) hydN ← / → mutS formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein
RA 1,849,373 A→T 5.5% V166E (GTG→GAG)  ygcH ← hypothetical protein
RA 1,892,019:1 +GC 100% intergenic (‑437/+54) gudP ← / ← ygdL predicted D‑glucarate transporter/conserved hypothetical protein
RA 2,256,801 T→C 5.4% K79K (AAA→AAG rpoC ← RNA polymerase, beta prime subunit
RA 2,256,819 A→G 7.6% G73G (GGT→GGC rpoC ← RNA polymerase, beta prime subunit
RA 2,256,831 C→T 6.0% E69E (GAG→GAA rpoC ← RNA polymerase, beta prime subunit
RA 2,256,859 C→T 5.8% R60H (CGT→CAT)  rpoC ← RNA polymerase, beta prime subunit
RA 2,359,867 G→A 28.4% noncoding (1228/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,359,876 C→T 32.2% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,518,841 A→T 7.2% T78T (ACT→ACA spoT ← bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 2,518,856 G→A 7.2% D73D (GAC→GAT spoT ← bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 2,567,260 T→C 5.9% intergenic (‑209/+21) mtlD ← / ← mtlA mannitol‑1‑phosphate dehydrogenase, NAD(P)‑binding/fused mannitol‑specific PTS enzyme IIABC components
RA 2,567,261 G→A 5.9% intergenic (‑210/+20) mtlD ← / ← mtlA mannitol‑1‑phosphate dehydrogenase, NAD(P)‑binding/fused mannitol‑specific PTS enzyme IIABC components
RA 2,726,575 A→G 6.9% L170L (TTG→CTG)  yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily
RA 2,726,579 T→G 6.5% S168S (TCA→TCC yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily
RA 2,726,583 C→G 7.0% R167P (CGT→CCT)  yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily
RA 2,726,588 A→C 7.5% I165M (ATT→ATG yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily
RA 2,726,600 G→C 7.2% A161A (GCC→GCG yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily
RA 2,726,603 A→C 7.7% L160L (CTT→CTG yheS ← fused predicted transporter subunits and ATP‑binding components of ABC superfamily

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ minE 251992 252057 66 21 [16] [16] 18 malZ maltodextrin glucosidase
* * ÷ minE 444383 444419 37 17 [15] [16] 19 kdpE DNA‑binding response regulator in two‑component regulatory system with KdpD
* * ÷ minE 865545 865591 47 17 [16] [16] 20 yciQ predicted inner membrane protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? minE = 706359 (0.840)30 (0.460)
+GATT
9/92 NT 49.0% coding (897/1431 nt) yaaJ predicted transporter
?minE = 1611756 9 (0.130)coding (1397/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? minE 26935 =32 (0.450)3 (0.050) 3/78 NT 7.4% intergenic (+62/‑394) dapB/carA dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
?minE 26998 = 50 (0.910)intergenic (+125/‑331) dapB/carA dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
* ? minE 95427 =92 (1.300)10 (0.160) 3/90 NT 11.1% coding (2409/2706 nt) secA preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon
?minE 95453 = 77 (1.210)coding (2435/2706 nt) secA preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon
* ? minE 204058 =NA (NA)4 (0.060) 3/92 NT NA noncoding (1463/1542 nt) rrsH 16S ribosomal RNA
?minE 204096 = NA (NA)noncoding (1501/1542 nt) rrsH 16S ribosomal RNA
* ? minE = 204740NA (NA)14 (0.240) 6/84 NT NA noncoding (157/2904 nt) rrlH 23S ribosomal RNA
?minE = 204751 NA (NA)noncoding (168/2904 nt) rrlH 23S ribosomal RNA
* ? minE = 205293NA (NA)6 (0.090) 3/92 NT NA noncoding (710/2904 nt) rrlH 23S ribosomal RNA
?minE = 205316 NA (NA)noncoding (733/2904 nt) rrlH 23S ribosomal RNA
* ? minE 436259 =64 (0.910)24 (0.370) 14/92 NT 30.2% intergenic (‑156/‑29) ybfF/seqA conserved hypothetical protein/regulatory protein for replication initiation
?minE = 2706018 52 (0.800)coding (836/837 nt) dam DNA adenine methylase
* ? minE = 43683394 (1.330)61 (0.860) 30/100 NT 41.8% coding (546/546 nt) seqA regulatory protein for replication initiation
?minE 1803907 = 76 (1.080)intergenic (+63/‑28) ygaH/mprA predicted inner membrane protein/DNA‑binding transcriptional regulator
* ? minE = 68980561 (0.860)5 (0.080) 3/92 NT 7.9% coding (968/1119 nt) hyaA hydrogenase 1, small subunit
?minE = 689836 60 (0.920)coding (999/1119 nt) hyaA hydrogenase 1, small subunit
* ? minE 825034 =64 (0.910)5 (0.080) 3/92 NT 7.8% coding (245/354 nt) ychN conserved hypothetical protein
?minE 825063 = 59 (0.910)coding (216/354 nt) ychN conserved hypothetical protein
* ? minE 981368 =59 (0.840)6 (0.100) 3/88 NT 9.8% coding (326/533 nt) ydfQ predicted lysozyme
?minE 981396 = 58 (0.930)coding (298/533 nt) ydfQ predicted lysozyme
* ? minE = 123070334 (0.480)3 (0.050) 3/94 NT 8.2% coding (2053/2061 nt) ptrB protease II
?minE = 1230732 35 (0.530)coding (2024/2061 nt) ptrB protease II
* ? minE 1637071 =60 (0.850)7 (0.110) 3/92 NT 10.6% intergenic (+95/‑444) acrD/yffB aminoglycoside/multidrug efflux system/conserved hypothetical protein
?minE 1637110 = 63 (0.970)intergenic (+134/‑405) acrD/yffB aminoglycoside/multidrug efflux system/conserved hypothetical protein
* ? minE = 182675655 (0.780)18 (0.260) 10/98 NT 22.2% intergenic (‑433/‑2) hydN/mutS formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein
?minE 2705183 = 72 (1.040)coding (1/837 nt) dam DNA adenine methylase
* ? minE = 193647154 (0.760)5 (0.080) 3/92 NT 9.6% coding (904/1734 nt) recJ ssDNA exonuclease, 5' ‑‑> 3'‑specific
?minE = 1936485 44 (0.680)coding (890/1734 nt) recJ ssDNA exonuclease, 5' ‑‑> 3'‑specific
* ? minE 2118619 =75 (1.060)6 (0.090) 4/92 NT 7.7% coding (133/2037 nt) yraM conserved hypothetical protein
?minE 2118653 = 74 (1.140)coding (167/2037 nt) yraM conserved hypothetical protein
* ? minE 2406673 =60 (0.850)4 (0.060) 3/92 NT 6.4% coding (788/2547 nt) cyaA adenylate cyclase
?minE 2406702 = 61 (0.940)coding (759/2547 nt) cyaA adenylate cyclase
* ? minE = 273615433 (0.470)4 (0.060) 3/88 NT 9.6% coding (1298/2115 nt) fusA protein chain elongation factor EF‑G
?minE = 2736178 46 (0.740)coding (1322/2115 nt) fusA protein chain elongation factor EF‑G
* ? minE = 273869254 (0.760)7 (0.110) 3/90 NT 13.4% intergenic (+466/‑63) tufA/rpsJ protein chain elongation factor EF‑Tu/30S ribosomal subunit protein S10
?minE = 2738700 42 (0.660)intergenic (+474/‑55) tufA/rpsJ protein chain elongation factor EF‑Tu/30S ribosomal subunit protein S10