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 161,068 A→C 24.0% intergenic (+47/‑149) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 234,984 G→T 18.2% I80I (ATC→ATA) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,985 A→T 8.4% I80N (ATC→AAC) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,990 G→T 13.8% F78L (TTC→TTA ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,994 G→T 26.6% S77* (TCA→TAA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,005 C→A 17.0% T73T (ACG→ACT) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,006 G→T 17.3% T73K (ACG→AAG) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,010 G→T 21.1% L72I (CTT→ATT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,019 C→A 29.6% V69L (GTA→TTA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,022 G→T 24.7% H68N (CAT→AAT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,036 G→T 19.2% S63Y (TCC→TAC)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 295,695 T→G 25.4% E317D (GAA→GAC paoC ← PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA 345,428 T→C 5.6% intergenic (+145/‑295) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 353,486 A→T 8.2% intergenic (+321/+16) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,489 C→T 7.7% intergenic (+324/+13) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,537 T→C 5.2% K289E (AAA→GAA)  cynR ← transcriptional activator of cyn operon; autorepressor
RA 360,156 C→G 7.5% intergenic (‑90/+505) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,157 T→G 7.2% intergenic (‑91/+504) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,172 T→A 5.3% intergenic (‑106/+489) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,173 C→A 9.6% intergenic (‑107/+488) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,181 G→C 5.3% intergenic (‑115/+480) 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 9.7% 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 370,632 A→G 5.0% intergenic (+295/‑283) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 370,703 A→G 5.0% intergenic (+366/‑212) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 613,891 T→A 8.7% L61Q (CTG→CAG)  fepE → regulator of length of O‑antigen component of lipopolysaccharide chains
RA 667,017 T→G 18.1% E15D (GAA→GAC holA ← DNA polymerase III, delta subunit
RA 772,664 A→C 7.1% K289N (AAA→AAC tolA → membrane anchored protein in TolA‑TolQ‑TolR complex
RA 877,980 G→T 5.3% Q71K (CAA→AAA)  deoR ← deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx
RA 1,191,676 C→T 5.1% H366H (CAC→CAT icd → e14 prophage; isocitrate dehydrogenase, specific for NADP+
RA 1,212,582 C→A 10.1% intergenic (+130/‑202) ymgC → / → ycgG Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 1,282,430 C→T 6.4% intergenic (+448/+92) 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 15.1% coding (27‑29/591 nt) pinR ← Rac prophage; putative site‑specific recombinase
RA 1,429,253 G→T 7.6% pseudogene (13/51 nt) ttcC ← pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA 1,460,458 T→C 5.1% pseudogene (810/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,467 G→A 6.0% pseudogene (819/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,887 G→C 8.0% pseudogene (1239/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,896 C→T 6.9% pseudogene (1248/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,628,207 G→A 100% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,676,007 G→C 6.8% A94G (GCG→GGG)  ydgC ← GlpM family inner membrane protein
RA 1,702,919 C→G 5.6% Q582E (CAA→GAA)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,702,966 T→A 10.3% R597R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,985,173 A→T 6.6% intergenic (‑73/+123) yecA ← / ← leuZ UPF0149 family protein/tRNA‑Leu
RA 2,036,746 G→T 7.3% intergenic (+367/+203) yodB → / ← serU cytochrome b561 homolog/tRNA‑Ser
RA 2,170,707 C→A 22.0% intergenic (‑24/+284) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,709 A→T 8.2% intergenic (‑26/+282) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,713 C→A 25.5% intergenic (‑30/+278) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,720 T→A 8.2% intergenic (‑37/+271) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,724 G→T 25.3% 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 11.4% intergenic (‑74/+234) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,178,919 G→T 6.7% intergenic (‑139/+84) thiM ← / ← rcnR hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA 2,178,937 A→T 8.5% intergenic (‑157/+66) thiM ← / ← rcnR hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA 2,298,128 C→T 7.5% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,400,223 A→C 7.9% intergenic (‑103/‑817) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA 2,463,906 C→A 19.1% Q433K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,910 G→T 18.9% R434I (AGA→ATA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,915 C→A 14.3% Q436K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,587,434 T→A 6.8% L595F (TTA→TTT tmcA ← elongator methionine tRNA (ac4C34) acetyltransferase
RA 2,598,122 T→G 9.0% L306R (CTT→CGT)  hyfC → hydrogenase 4, membrane subunit
RA 2,719,168 A→T 6.3% intergenic (‑63/+260) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
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 14.8% H361N (CAC→AAC)  gabD → succinate‑semialdehyde dehydrogenase I, NADP‑dependent
RA 2,811,275 T→G 6.8% intergenic (‑56/+143) argQ ← / ← argZ tRNA‑Arg/tRNA‑Arg
RA 2,834,252 A→T 6.9% E457V (GAG→GTG)  ascF → fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA 2,908,686 G→T 18.2% E91* (GAA→TAA)  barA → hybrid sensory histidine kinase, in two‑component regulatory system with UvrY
RA 3,039,409 T→G 16.1% intergenic (‑149/+118) ygfF ← / ← gcvP putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA 3,080,755 T→G 26.1% F231V (TTC→GTC)  metK → S‑adenosylmethionine synthetase
RA 3,203,148 T→G 12.9% K252T (AAG→ACG)  tsaD ← tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein
RA 3,385,487 A→T 6.2% intergenic (‑100/+330) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,696 T→A 6.3% intergenic (‑309/+121) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,416,890 T→G 5.2% noncoding (12/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,439,422 G→T 7.9% I26I (ATC→ATA rplF ← 50S ribosomal subunit protein L6
RA 3,498,214 T→G 11.1% intergenic (+72/+80) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
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 3,602,056 T→G 6.8% intergenic (+47/+55) zntA → / ← tusA zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase
RA 3,602,367 T→A 9.2% intergenic (‑11/‑210) tusA ← / → yhhQ mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase/DUF165 family inner membrane protein
RA 3,779,316 G→T 9.6% D233Y (GAT→TAT)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,807,003 G→T 5.0% V305F (GTT→TTT)  dfp → fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
RA 3,816,601 A→T 100% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,822,339 A→C 7.6% Q12P (CAA→CCA)  xanP → xanthine permease
RA 3,901,867 T→G 6.5% intergenic (‑141/+42) pstB ← / ← pstA phosphate transporter subunit/phosphate transporter subunit
RA 3,960,036 G→A 86.5% R87H (CGC→CAC)  rho → transcription termination factor
RA 4,143,375 A→G 6.5% intergenic (‑349/+249) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,285,857 T→C 5.9% intergenic (+135/+396) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,285,892 A→G 5.4% intergenic (+170/+361) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,297,846 C→A 74.2% M150I (ATG→ATT alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,603,125 A→C 7.9% T300P (ACG→CCG)  yjjU → putative patatin‑like family phospholipase
RA 4,604,320 T→C 5.0% intergenic (+243/+177) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme
RA 4,604,397 G→A 5.2% intergenic (+320/+100) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373874 375100 1227 140 [138] [139] 148 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100616 4101519 904 140 [138] [137] 140 tpiA tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =176 (0.780)125 (0.560) 81/276 NT 41.5% 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)22160 (104.820)
+TTAATTAA
197/260 NT 99.0% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 228 (1.020)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =229 (1.020)20692 (138.750)
+46 bp
184/184 NT 99.3% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 184 (0.820)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 376716 =NA (NA)153 (0.680) 102/276 NT 75.0% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 51 (0.230)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)182 (0.810) 107/276 NT 77.8% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 52 (0.230)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 776825 =113 (0.500)19 (0.090)
+G
4/274 NT 12.4% noncoding (1/76 nt) lysZ tRNA‑Lys
?CP009273 = 2514487 157 (0.700)noncoding (215/1345 nt) IS186 repeat region
* ? CP009273 = 776902131 (0.580)7 (0.040) 4/236 NT 5.5% intergenic (+2/‑131) lysZ/lysQ tRNA‑Lys/tRNA‑Lys
?CP009273 2514846 = 130 (0.680)noncoding (574/1345 nt) IS186 repeat region
* ? CP009273 1203246 =13 (0.060)158 (0.800) 87/244 NT 93.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 12 (0.060)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326113 (0.060)177 (0.890) 102/244 NT 93.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 12 (0.060)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 2007609220 (0.980)32 (0.150) 23/264 NT 14.7% coding (900/1659 nt) fliF flagellar basal‑body MS‑ring and collar protein
?CP009273 2021385 = 162 (0.750)coding (114/1695 nt) yedQ putative membrane‑anchored diguanylate cyclase
* ? CP009273 = 2811301153 (0.680)8 (0.040) 5/236 NT 5.3% intergenic (‑82/+117) argQ/argZ tRNA‑Arg/tRNA‑Arg
?CP009273 2811851 = 155 (0.810)noncoding (58/77 nt) argV tRNA‑Arg
* ? CP009273 4532499 =114 (0.510)84 (0.400) 53/258 NT 44.6% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 102 (0.490)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 4532507119 (0.530)82 (0.390) 54/258 NT 43.5% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 102 (0.490)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)