breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 10,245 G→A 5.1% L84L (CTG→TTG)  satP ← succinate‑acetate transporter
RA 164,620 C→T 5.7% intergenic (+86/‑110) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 164,621 A→G 5.7% intergenic (+87/‑109) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 193,565 C→T 5.0% C15C (TGC→TGT dxr → 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
RA 217,593 G→T 5.1% P395T (CCA→ACA)  proS ← prolyl‑tRNA synthetase
RA 251,639 A→G 5.5% T248A (ACG→GCG)  dinB → DNA polymerase IV
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 267,148 Δ1 bp 5.1% intergenic (‑181/+36) ykfK ← / ← yafZ CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related/CP4‑6 prophage; conserved protein
RA 301,237 C→T 5.0% T217T (ACG→ACA paoB ← PaoABC aldehyde oxidoreductase, FAD‑containing subunit
RA 349,828 G→A 6.6% intergenic (+256/‑184) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 508,745 T→G 9.5% intergenic (+186/+130) ybaQ → / ← copA putative DNA‑binding transcriptional regulator/copper transporter
RA 511,232 C→A 5.4% E50* (GAA→TAA)  copA ← copper transporter
RA 632,082 C→A 5.6% intergenic (+83/‑100) cstA → / → ybdD carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
RA 823,524 G→A 5.4% Y72Y (TAC→TAT clsB ← cardiolipin synthase 2
RA 828,135 C→T 6.2% G283R (GGG→AGG)  ybhF ← putative ABC transporter ATPase
RA 870,063 T→C 5.1% I218T (ATA→ACA)  gsiB → glutathione ABC transporter periplasmic binding protein
RA 891,882 C→G 5.8% H233Q (CAC→CAG nfsA → nitroreductase A, NADPH‑dependent, FMN‑dependent
RA 892,441 G→A 6.3% A159T (GCG→ACG) ‡ rimK → ribosomal protein S6 modification protein
RA 892,443 G→C 6.3% A159A (GCG→GCC) ‡ rimK → ribosomal protein S6 modification protein
RA 892,455 G→C 6.2% V163V (GTG→GTC rimK → ribosomal protein S6 modification protein
RA 892,457 T→A 6.6% I164N (ATT→AAT)  rimK → ribosomal protein S6 modification protein
RA 892,459 G→C 6.6% D165H (GAC→CAC)  rimK → ribosomal protein S6 modification protein
RA 1,011,082 C→A 5.7% S373R (AGC→AGA uup → replication regulatory ABC‑F family DNA‑binding ATPase
RA 1,112,767 C→T 6.0% G635G (GGC→GGT opgH → OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA 1,141,656 T→A 7.3% E904D (GAA→GAT rne ← endoribonuclease; RNA‑binding protein;RNA degradosome binding protein
RA 1,153,208 T→C 7.2% intergenic (+28/‑92) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,213 T→A 6.2% intergenic (+33/‑87) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,214 T→A 6.8% intergenic (+34/‑86) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,153,219 G→A 6.4% intergenic (+39/‑81) fabF → / → pabC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,176,906 C→T 6.6% H96H (CAC→CAT lolD → outer membrane‑specific lipoprotein transporter subunit
RA 1,224,239 A→T 8.0% intergenic (+332/+40) ycgI → / ← minE pseudogene/cell division topological specificity factor
RA 1,224,242 A→T 5.8% intergenic (+335/+37) ycgI → / ← minE pseudogene/cell division topological specificity factor
RA 1,287,122 T→G 8.2% noncoding (115/171 nt)
R19R (AGG→CGG) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,123 G→C 6.8% noncoding (114/171 nt)
R18R (CGC→CGG) ‡
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,124 C→A 6.8% noncoding (113/171 nt)
R18L (CGC→CTC) ‡
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,672 C→T 100% intergenic (‑50/+110) tyrT ← / ← purU tRNA‑Tyr/formyltetrahydrofolate hydrolase
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,331,082 C→A 5.3% A12E (GCA→GAA)  topA → DNA topoisomerase I, omega subunit
MC JC 1,335,035 Δ726 bp 100% ymiAyciX ymiA, yciX
RA 1,344,033 A→G 6.7% L105P (CTG→CCG)  yciT ← global regulator of transcription; DeoR family
RA 1,345,632 T→C 6.3% T371A (ACG→GCG)  gmr ← cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability
RA 1,347,745 C→T 5.4% E390K (GAA→AAA)  rnb ← ribonuclease II
RA 1,352,369 C→T 5.0% R89H (CGT→CAT)  sapF ← antimicrobial peptide ABC transporter ATPase
RA 1,416,980 C→A 6.6% G136V (GGC→GTC)  recE ← Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
RA 1,568,915 G→A 5.7% intergenic (‑92/+39) yddW ← / ← gadC liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA 1,568,917 A→T 5.9% intergenic (‑94/+37) yddW ← / ← gadC liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA 1,568,919 T→C 5.9% intergenic (‑96/+35) yddW ← / ← gadC liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter
RA 1,693,416 A→G 5.2% L283P (CTG→CCG)  uidB ← glucuronide transporter
RA 1,720,364 G→T 5.8% intergenic (+21/+26) slyB → / ← slyA outer membrane lipoprotein/global transcriptional regulator
RA 1,723,266 G→A 5.4% W382* (TGG→TGA ydhK → putative efflux protein (PET) component of YdhJK efflux pump
RA 1,753,390 C→A 5.2% T147T (ACG→ACT ydhV ← putative oxidoreductase subunit
RA 1,782,643 A→T 5.3% N417Y (AAC→TAC)  ydiS → putative oxidoreductase
RA 1,953,532 C→T 5.3% Q31* (CAG→TAG)  cmoB → tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA 1,963,803 G→A 6.9% A416A (GCC→GCT flhA ← putative flagellar export pore protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 1,987,442 Δ1 bp 8.2% intergenic (+14/+65) ftnB → / ← yecJ ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA 1,987,450:1 +A 8.3% intergenic (+22/+57) ftnB → / ← yecJ ferritin B, putative ferrous iron reservoir/DUF2766 family protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,216,925 A→G 5.7% P161P (CCT→CCC yehX ← putative ABC transporter ATPase
RA 2,317,780 T→C 6.1% K699K (AAA→AAG rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,374,672 G→A 5.2% T111M (ACG→ATG)  menE ← O‑succinylbenzoate‑CoA ligase
RA 2,560,996 G→T 13.9% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,726,044 T→G 9.0% intergenic (‑298/+25) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,726,046 A→C 6.6% intergenic (‑300/+23) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,745,019 T→A 5.7% K107N (AAA→AAT) ‡ trmD ← tRNA m(1)G37 methyltransferase, SAM‑dependent
RA 2,745,020 T→A 5.2% K107I (AAA→ATA) ‡ trmD ← tRNA m(1)G37 methyltransferase, SAM‑dependent
RA 3,020,511 C→G 5.4% intergenic (+22/‑29) ssnA → / → ygfM putative chlorohydrolase/aminohydrolase/putative oxidoreductase
RA 3,037,430 A→G 5.1% L226P (CTG→CCG)  recJ ← ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA 3,045,803 C→T 6.9% Q33Q (CAG→CAA ygfF ← putative NAD(P)‑dependent oxidoreductase
RA 3,114,526 G→T 6.3% intergenic (‑174/+24) pppA ← / ← sslE bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase
RA 3,114,527 A→C 6.2% intergenic (‑175/+23) pppA ← / ← sslE bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase
RA 3,114,533 T→G 5.1% intergenic (‑181/+17) pppA ← / ← sslE bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase
RA 3,269,956 T→C 8.6% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,269,969 A→C 7.3% intergenic (+367/+247) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,272,209 A→G 6.1% I181I (ATT→ATC garR ← tartronate semialdehyde reductase
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,698,203 G→T 7.4% A60S (GCA→TCA)  bcsF → DUF2636 family cellulose production small membrane protein
RA 3,708,428 T→A 5.5% intergenic (‑723/+188) dppA ← / ← proK dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
RA 3,772,467 C→T 6.3% L63L (CTG→TTG)  mtlA → mannitol‑specific PTS enzyme: IIA, IIB and IIC components
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,262,250 G→C 5.8% G194G (GGG→GGC dusA → tRNA‑dihydrouridine synthase A
RA 4,262,255 G→C 5.8% S196T (AGC→ACC)  dusA → tRNA‑dihydrouridine synthase A
RA 4,296,060 C→T 29.3% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,482,758 G→A 6.4% H360H (CAC→CAT valS ← valyl‑tRNA synthetase
RA 4,495,814 C→T 5.5% W132* (TGG→TGA ahr ← broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing
RA 4,592,095 A→T 5.1% K147* (AAA→TAA)  tsr → methyl‑accepting chemotaxis protein I, serine sensor receptor
RA 4,606,354 G→A 11.5% noncoding (48/87 nt) leuQ ← tRNA‑Leu

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 131559 134211 2653 36 [34] [32] 35 [acnB] [acnB]
* * ÷ NC_000913 2066258–2066626 2066626 1–369 36 [34] [34] 36 [insH1] [insH1]
* * ÷ NC_000913 3423749–3424234 3424540–3424238 5–792 35 [33] [34] 36 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =34 (0.380)53 (0.670) 48/224 NT 58.6% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 45 (0.570)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780533 (0.370)38 (0.480) 34/224 NT 50.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 45 (0.570)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)94 (1.070) 69/248 NT 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 258079269 (0.760)4 (0.050) 4/246 NT 5.3% coding (1157/2004 nt) tktB transketolase 2, thiamine triphosphate‑binding
?NC_000913 = 2580804 76 (0.880)coding (1169/2004 nt) tktB transketolase 2, thiamine triphosphate‑binding
* ? NC_000913 2627637 =62 (0.690)4 (0.050) 4/244 NT 5.8% coding (1302/2244 nt) yfgF cyclic‑di‑GMP phosphodiesterase, anaerobic
?NC_000913 2627672 = 70 (0.810)coding (1267/2244 nt) yfgF cyclic‑di‑GMP phosphodiesterase, anaerobic
* ? NC_000913 = 2856434NA (NA)3 (0.040) 3/236 NT NA noncoding (9/24 nt) REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences
?NC_000913 = 2856440 NA (NA)noncoding (15/24 nt) REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences
* ? NC_000913 = 3890165100 (1.110)7 (0.080) 7/236 NT 6.7% intergenic (+20/‑71) tnaA/tnaB tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity
?NC_000913 = 3890174 104 (1.250)intergenic (+29/‑62) tnaA/tnaB tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity
* ? NC_000913 4542682 =100 (1.110)9 (0.110) 9/238 NT 8.2% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 109 (1.300)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 4542690108 (1.200)18 (0.210) 16/238 NT 14.7% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 109 (1.300)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)