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 124,092 A→C 5.8% intergenic (+18/‑307) aceF → / → lpd pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2/lipoamide dehydrogenase, E3 component is part of three enzyme complexes
RA 234,984 G→T 13.7% I80I (ATC→ATA ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,994 G→T 21.7% S77* (TCA→TAA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,006 G→T 11.2% T73K (ACG→AAG)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,010 G→T 21.9% L72I (CTT→ATT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,019 C→A 18.1% V69L (GTA→TTA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,022 G→T 18.8% H68N (CAT→AAT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 345,353 A→G 7.8% intergenic (+70/‑370) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 345,384 G→C 5.4% intergenic (+101/‑339) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 345,387 G→A 5.1% intergenic (+104/‑336) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 345,428 T→C 7.9% intergenic (+145/‑295) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 353,486 A→T 8.8% intergenic (+321/+16) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,489 C→T 8.2% intergenic (+324/+13) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 360,157 T→G 8.6% intergenic (‑91/+504) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,173 C→A 7.0% intergenic (‑107/+488) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,197 T→A 6.4% intergenic (‑131/+464) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,752 A→G 100% V331A (GTG→GCG)  lacI ← DNA‑binding transcriptional repressor
JC 361,139 +GCCA 9.3% coding (605/1083 nt) lacI ← DNA‑binding transcriptional repressor
RA 361,806 G→A 100% intergenic (‑63/+14) lacI ← / ← mhpR DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA 370,703 A→G 5.1% intergenic (+366/‑212) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 450,333 A→T 8.6% intergenic (+88/‑256) bolA → / → tig stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA 776,694 T→A 5.6% intergenic (+16/‑131) lysY → / → lysZ tRNA‑Lys/tRNA‑Lys
RA 877,776 A→C 5.5% F139V (TTT→GTT)  deoR ← deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA 1,118,506 A→T 11.5% L75Q (CTA→CAA)  yceB ← lipoprotein, DUF1439 family
RA 1,282,421 A→T 14.3% intergenic (+439/+101) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
JC JC 1,376,043 IS5 (–) +4 bp 100% pseudogene (10‑13/126 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
JC JC 1,427,903 IS3 (–) +3 bp 21.6% coding (27‑29/591 nt) pinR ← Rac prophage; putative site‑specific recombinase
RA 1,460,752 C→T 6.6% pseudogene (1104/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,628,207 G→A 95.0% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,702,966 T→A 8.0% R597R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,062 T→A 10.6% R629R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,071 A→T 8.3% A632A (GCA→GCT rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,101 C→G 9.7% A642A (GCC→GCG rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 2,170,708 G→T 9.6% intergenic (‑25/+283) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,713 C→A 28.9% intergenic (‑30/+278) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,724 G→T 31.2% intergenic (‑41/+267) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,757 T→A 14.6% intergenic (‑74/+234) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,758 C→A 13.5% intergenic (‑75/+233) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,178,937 A→T 10.2% intergenic (‑157/+66) thiM ← / ← rcnR hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA 2,298,128 C→T 6.4% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,492 A→G 5.0% intergenic (+620/+95) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,303,607 A→C 6.9% L93R (CTG→CGG)  ada ← fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA 2,463,906 C→A 19.9% Q433K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,910 G→T 17.4% R434I (AGA→ATA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,915 C→A 12.8% Q436K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,711,673 A→C 9.2% V72G (GTT→GGT)  yfiF ← putative methyltransferase
JC 2,713,645 +CCTGCGC 11.7% coding (334/2661 nt) pka → protein lysine acetyltransferase
RA 2,719,426 T→C 100% intergenic (‑321/+2) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,785,712 C→A 29.3% H361N (CAC→AAC)  gabD → succinate‑semialdehyde dehydrogenase I, NADP‑dependent
RA 2,811,504 T→C 5.4% intergenic (‑10/+53) argZ ← / ← argY tRNA‑Arg/tRNA‑Arg
JC 2,811,717 Δ134 bp 5.5% [argV] [argV]
RA 2,834,252 A→T 7.8% E457V (GAG→GTG)  ascF → fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA 2,834,267 A→T 5.8% E462V (GAG→GTG)  ascF → fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA 2,835,291 T→G 13.1% C315G (TGC→GGC)  ascB → cryptic 6‑phospho‑beta‑glucosidase
RA 3,263,315 T→C 6.0% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,263,460 C→A 12.5% intergenic (+499/+115) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,263,502 C→T 8.4% intergenic (+541/+73) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,385,479 C→G 10.4% intergenic (‑92/+338) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,487 A→T 7.5% intergenic (‑100/+330) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,516 A→T 11.8% intergenic (‑129/+301) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,518 G→C 10.4% intergenic (‑131/+299) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,416,890 T→G 9.1% noncoding (12/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,416,899 A→G 5.7% noncoding (3/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,449,090 C→A 5.5% P52T (CCA→ACA)  gspC → general secretory pathway component, cryptic
RA 3,469,859 G→T 9.6% intergenic (‑60/+107) yheO ← / ← fkpA putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA 3,519,657 G→T 100% intergenic (‑149/‑171) nudE ← / → yrfF adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA 3,546,339 C→A 11.2% intergenic (‑507/‑105) malP ← / → malT maltodextrin phosphorylase/mal regulon transcriptional activator
RA 3,547,642 T→A 12.9% L400Q (CTG→CAG)  malT → mal regulon transcriptional activator
RA 3,721,485 T→G 10.7% Y416S (TAC→TCC)  xylB ← xylulokinase
RA 3,786,687 C→A 5.8% L119F (TTG→TTT yibB ← YibB family protein, function unknown
RA 3,816,601 A→T 94.3% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,822,339 A→C 9.9% Q12P (CAA→CCA) ‡ xanP → xanthine permease
RA 3,822,340 A→C 14.5% Q12H (CAA→CAC) ‡ xanP → xanthine permease
RA 3,871,017 A→T 6.7% intergenic (‑192/+48) yidB ← / ← gyrB DUF937 family protein/DNA gyrase, subunit B
RA 3,960,036 G→A 91.5% R87H (CGC→CAC)  rho → transcription termination factor
RA 4,143,375 A→G 6.6% intergenic (‑349/+249) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,143,544 C→T 6.6% intergenic (‑518/+80) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,297,846 C→A 86.4% M150I (ATG→ATT alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,315,765 A→G 5.5% intergenic (‑207/+451) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,361,085 A→C 9.3% N82H (AAC→CAC)  groL → Cpn60 chaperonin GroEL, large subunit of GroESL
RA 4,411,145 T→G 10.5% L450R (CTG→CGG)  ulaA → L‑ascorbate‑specific enzyme IIC permease component of PTS
RA 4,557,158 T→C 5.3% G393G (GGA→GGG mdtM ← multidrug efflux system protein
RA 4,604,240 T→A 6.3% intergenic (+163/+257) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme
RA 4,604,261 A→G 7.9% intergenic (+184/+236) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373843 375099 1257 140 [137] [137] 141 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100623 4101505 883 141 [135] [138] 141 tpiA tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =133 (0.600)124 (0.560) 69/276 NT 48.2% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 = 360278NA (NA)21752 (104.610)
+TTAATTAA
196/260 NT 99.0% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 224 (1.010)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =204 (0.920)20871 (142.290)
+46 bp
183/184 NT 99.4% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 193 (0.870)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 = 361823224 (1.010)11 (0.050)
+TTAATTAA
6/260 NT 5.3% coding (831/834 nt) mhpR mhp operon transcriptional activator
?CP009273 4033991 = 194 (0.880)noncoding (115/120 nt) rrfA 5S ribosomal RNA of rrnA operon
* ? CP009273 376716 =NA (NA)189 (0.860) 110/276 NT 85.5% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 32 (0.140)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)222 (1.010) 118/276 NT 87.4% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 32 (0.140)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 776825 =139 (0.630)20 (0.090)
+G
7/274 NT 12.3% noncoding (1/76 nt) lysZ tRNA‑Lys
?CP009273 = 2514488 147 (0.670)noncoding (216/1345 nt) IS186 repeat region
* ? CP009273 1203246 =6 (0.030)164 (0.840) 94/244 NT 93.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 19 (0.100)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032616 (0.030)195 (1.000) 107/244 NT 94.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 19 (0.100)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 3385461221 (1.000)14 (0.080) 13/210 NT 8.4% noncoding (27/308 nt) REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences
?CP009273 3385736 = 138 (0.820)noncoding (302/308 nt) REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences
* ? CP009273 4532499 =173 (0.780)22 (0.110) 15/258 NT 10.8% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 201 (0.970)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 4532507178 (0.810)22 (0.110) 13/258 NT 10.7% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 201 (0.970)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)