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 27,603 T→G 10.2% F104C (TTT→TGT)  rihC → ribonucleoside hydrolase 3
RA 68,486 T→G 22.0% L217V (TTG→GTG)  yabI → DedA family inner membrane protein
RA 107,220 A→T 14.3% K819* (AAA→TAA)  secA → preprotein translocase subunit, ATPase
RA 234,984 G→T 14.4% I80I (ATC→ATA) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,985 A→T 11.8% I80N (ATC→AAC) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,990 G→T 13.4% F78L (TTC→TTA ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,994 G→T 18.8% S77* (TCA→TAA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,005 C→A 15.0% T73T (ACG→ACT) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,006 G→T 11.9% T73K (ACG→AAG) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,010 G→T 17.6% L72I (CTT→ATT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,019 C→A 21.6% V69L (GTA→TTA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,022 G→T 19.7% H68N (CAT→AAT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,036 G→T 17.6% S63Y (TCC→TAC)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 283,636 A→C 9.1% Q379H (CAA→CAC yagH → CP4‑6 prophage; putative xylosidase/arabinosidase
RA 295,695 T→G 20.5% E317D (GAA→GAC paoC ← PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA 345,384 G→C 5.5% intergenic (+101/‑339) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 353,486 A→T 7.3% intergenic (+321/+16) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,489 C→T 5.8% intergenic (+324/+13) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 360,114 A→T 5.4% intergenic (‑48/+547) 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 10.1% 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 450,329 C→G 15.9% intergenic (+84/‑260) bolA → / → tig stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA 576,183 G→T 10.1% intergenic (‑282/‑107) ylcI ← / → nohD DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein
RA 772,664 A→C 14.0% K289N (AAA→AAC tolA → membrane anchored protein in TolA‑TolQ‑TolR complex
RA 816,078 C→G 6.2% intergenic (+34/‑171) ybhL → / → ybhM UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA 816,095 T→A 7.5% intergenic (+51/‑154) ybhL → / → ybhM UPF0005 family inner membrane protein/UPF0005 family inner membrane protein
RA 847,954 A→C 5.2% L34V (TTA→GTA)  ybiP ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 910,654 C→G 7.3% intergenic (‑341/+154) ybjE ← / ← aqpZ putative transporter/aquaporin Z
JC JC 919,057 IS5 (–) +4 bp 45.4% coding (338‑341/2277 nt) clpA → ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA 1,092,897 C→T 8.5% intergenic (+612/+124) ycdU → / ← serX putative inner membrane protein/tRNA‑Ser
RA 1,118,469 G→C 5.8% F87L (TTC→TTG yceB ← lipoprotein, DUF1439 family
RA 1,282,337 A→T 7.1% intergenic (+355/+185) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,282,421 A→T 13.9% intergenic (+439/+101) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,282,439 A→T 9.9% intergenic (+457/+83) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,282,605 G→A 6.2% noncoding (88/171 nt)
R10* (CGA→TGA) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,282,608 T→C 5.7% noncoding (85/171 nt)
T9A (ACT→GCT) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
JC JC 1,376,043 IS5 (–) +4 bp 39.5% pseudogene (10‑13/126 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
JC JC 1,427,903 IS3 (–) +3 bp 13.8% coding (27‑29/591 nt) pinR ← Rac prophage; putative site‑specific recombinase
RA 1,429,253 G→T 8.5% pseudogene (13/51 nt) ttcC ← pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA 1,454,118 A→T 5.8% I270F (ATT→TTT)  paaH → 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA 1,460,593 C→G 7.2% pseudogene (945/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,602 T→C 6.7% pseudogene (954/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,752 C→T 9.8% pseudogene (1104/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,761 A→G 10.8% pseudogene (1113/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,819 G→A 5.1% pseudogene (1171/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,460,861 G→A 5.2% pseudogene (1213/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,516,408 T→G 6.2% E305D (GAA→GAC yncD ← putative iron outer membrane transporter
RA 1,628,207 G→A 41.7% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,670,108 A→C 6.7% V170V (GTT→GTG pntB ← pyridine nucleotide transhydrogenase, beta subunit
RA 1,673,368 G→T 6.4% E229* (GAA→TAA)  ydgH → DUF1471 family periplasmic protein
RA 1,673,380 T→A 7.3% S233T (TCA→ACA) ‡ ydgH → DUF1471 family periplasmic protein
RA 1,673,381 C→A 8.0% S233* (TCA→TAA) ‡ ydgH → DUF1471 family periplasmic protein
RA 1,701,282 A→C 5.7% Q36P (CAG→CCG)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,701,291 T→G 8.6% L39R (CTG→CGG)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,702,966 T→A 7.2% R597R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,101 C→G 8.4% A642A (GCC→GCG rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,795,380 A→T 52.8% V483E (GTA→GAA)  thrS ← threonyl‑tRNA synthetase
RA 1,796,428 C→A 14.1% V134F (GTC→TTC)  thrS ← threonyl‑tRNA synthetase
RA 1,823,835 A→C 7.5% W53G (TGG→GGG)  astD ← succinylglutamic semialdehyde dehydrogenase
RA 1,859,012 C→G 10.7% intergenic (+21/+27) yeaD → / ← yeaE D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA 1,863,933 A→C 6.3% K241T (AAG→ACG)  yeaH → UPF0229 family protein
RA 2,068,168 T→G 6.4% intergenic (+29/‑92) flu → / → yeeR CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein
RA 2,170,708 G→T 7.3% 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 21.1% 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 24.7% 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 9.9% 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 9.1% intergenic (‑75/+233) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,178,915 C→G 9.7% intergenic (‑135/+88) thiM ← / ← rcnR hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA 2,222,655 C→G 7.4% intergenic (+111/+262) yohP → / ← dusC uncharacterized protein/tRNA‑dihydrouridine synthase C
RA 2,298,128 C→T 11.8% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,159 T→C 8.2% intergenic (+287/+428) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,492 A→G 6.1% intergenic (+620/+95) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,303,607 A→C 5.6% L93R (CTG→CGG)  ada ← fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA 2,463,906 C→A 12.6% Q433K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,910 G→T 15.0% R434I (AGA→ATA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,914 T→A 10.4% N435K (AAT→AAA gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,915 C→A 11.4% Q436K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,598,079 C→A 11.7% L292I (CTC→ATC)  hyfC → hydrogenase 4, membrane subunit
RA 2,711,673 A→C 9.2% V72G (GTT→GGT)  yfiF ← putative methyltransferase
JC 2,713,645 +CCTGCGC 64.9% 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 8.7% H361N (CAC→AAC)  gabD → succinate‑semialdehyde dehydrogenase I, NADP‑dependent
RA 2,811,408 T→A 5.9% intergenic (‑189/+10) argQ ← / ← argZ tRNA‑Arg/tRNA‑Arg
RA 2,835,291 T→G 8.9% C315G (TGC→GGC)  ascB → cryptic 6‑phospho‑beta‑glucosidase
RA 2,940,829 A→T 9.1% intergenic (+7/‑27) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 3,039,409 T→G 14.5% 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 3,263,502 C→T 5.1% intergenic (+541/+73) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,275,236 G→T 5.6% intergenic (+252/‑99) agaA → / → agaS pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase/tagatose‑6‑phosphate ketose/aldose isomerase
RA 3,385,479 C→G 8.0% intergenic (‑92/+338) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,696 T→A 5.4% intergenic (‑309/+121) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,439,422 G→T 7.9% I26I (ATC→ATA rplF ← 50S ribosomal subunit protein L6
RA 3,439,443 G→T 6.9% I19I (ATC→ATA rplF ← 50S ribosomal subunit protein L6
RA 3,469,871 T→A 6.8% intergenic (‑72/+95) yheO ← / ← fkpA putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA 3,498,214 T→G 10.1% intergenic (+72/+80) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,498,239 A→C 7.3% intergenic (+97/+55) 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 3,525,215 A→C 11.8% L195R (CTG→CGG)  yhgE ← DUF4153 family putative inner membrane protein
RA 3,546,282 A→T 9.7% intergenic (‑450/‑162) malP ← / → malT maltodextrin phosphorylase/mal regulon transcriptional activator
RA 3,546,300 G→T 16.6% intergenic (‑468/‑144) malP ← / → malT maltodextrin phosphorylase/mal regulon transcriptional activator
RA 3,633,969 T→G 9.1% intergenic (+64/‑253) uspA → / → dtpB universal stress global response regulator/dipeptide and tripeptide permease B
RA 3,721,485 T→G 11.9% Y416S (TAC→TCC)  xylB ← xylulokinase
RA 3,779,281 C→G 6.8% A221G (GCT→GGT)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,779,316 G→T 7.6% D233Y (GAT→TAT)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,779,319 G→T 7.9% E234* (GAA→TAA)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,786,687 C→A 8.8% L119F (TTG→TTT yibB ← YibB family protein, function unknown
RA 3,803,561 T→G 7.2% F126C (TTT→TGT)  coaD → pantetheine‑phosphate adenylyltransferase
RA 3,816,601 A→T 40.1% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,822,340 A→C 13.3% Q12H (CAA→CAC xanP → xanthine permease
RA 3,870,977 T→A 6.4% intergenic (‑152/+88) yidB ← / ← gyrB DUF937 family protein/DNA gyrase, subunit B
RA 3,872,511 A→C 5.6% V323V (GTT→GTG gyrB ← DNA gyrase, subunit B
RA 3,926,578 T→G 10.8% intergenic (+34/‑133) kup → / → rbsD potassium transporter/putative cytoplasmic sugar‑binding protein
RA 3,952,817 T→G 10.3% intergenic (+12/+75) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,952,842 A→C 5.7% intergenic (+37/+50) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,952,861 T→A 7.8% intergenic (+56/+31) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,960,036 G→A 26.7% R87H (CGC→CAC)  rho → transcription termination factor
RA 4,080,325 G→T 10.5% intergenic (+116/‑37) fdhD → / → yiiG formate dehydrogenase formation protein/DUF3829 family lipoprotein
RA 4,080,364 G→T 10.2% M1M (ATG→ATT) † yiiG → DUF3829 family lipoprotein
RA 4,143,375 A→G 5.7% intergenic (‑349/+249) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,286,214 T→C 5.1% intergenic (+492/+39) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,297,846 C→A 20.7% M150I (ATG→ATT alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,315,765 A→G 5.1% intergenic (‑207/+451) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,382,288 A→C 7.2% intergenic (+36/‑1) glyV → / → glyX tRNA‑Gly/tRNA‑Gly
RA 4,575,840 A→C 5.6% pseudogene (793/3567 nt) hsdR ← pseudogene, premature stop codon, host restriction; endonuclease R
RA 4,604,195 A→G 6.4% intergenic (+118/+302) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373825 375115 1291 202 [192] [189] 195 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100602 4101513 912 193 [192] [191] 195 [cdh]–tpiA [cdh],tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =187 (0.640)143 (0.490) 86/276 NT 43.3% 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)10019 (36.510)
+TTAATTAA
197/260 NT 97.6% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 260 (0.890)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =326 (1.120)9244 (47.760)
+46 bp
182/184 NT 97.9% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 259 (0.890)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 376716 =NA (NA)78 (0.270) 52/276 NT 27.6% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 205 (0.700)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)62 (0.210) 37/276 NT 23.3% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 204 (0.700)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 1203246 =42 (0.140)206 (0.800) 100/244 NT 82.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 50 (0.190)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 1203252 =46 (0.160)3 (0.010)
+C
3/274 NT 5.9% coding (296/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205070 = 51 (0.180)pseudogene (6/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326145 (0.150)220 (0.850) 115/244 NT 83.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 50 (0.190)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 128254097 (0.330)11 (0.040) 7/236 NT 7.6% noncoding (153/171 nt) rttR rtT sRNA, processed from tyrT transcript
?CP009273 1283013 = 184 (0.740)noncoding (66/85 nt) tyrT tRNA‑Tyr
* ? CP009273 = 2007609207 (0.710)21 (0.080) 12/264 NT 8.9% coding (900/1659 nt) fliF flagellar basal‑body MS‑ring and collar protein
?CP009273 2021385 = 233 (0.840)coding (114/1695 nt) yedQ putative membrane‑anchored diguanylate cyclase