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 53,272 T→G 5.9% M49L (ATG→CTG)  pdxA ← 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent
RA 59,052 C→T 6.1% pseudogene (579/579 nt)
pseudogene (1/228 nt)
yabP →
yabP →
pseudogene, pentapeptide repeats‑containing
pseudogene, pentapeptide repeats‑containing
RA 62,377 A→G 5.4% Y296Y (TAT→TAC rapA ← RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
RA 151,715 G→A 5.3% R173C (CGC→TGC)  yadL ← putative fimbrial‑like adhesin protein
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 466,420 T→C 5.4% E298G (GAG→GGG)  ybaE ← putative ABC transporter periplasmic binding protein
RA 543,091 G→C 5.5% intergenic (+58/+170) glxK → / ← allE glycerate kinase II/S‑ureidoglycine aminohydrolase
RA 543,094 G→C 5.7% intergenic (+61/+167) glxK → / ← allE glycerate kinase II/S‑ureidoglycine aminohydrolase
RA 584,237 A→G 5.0% D186G (GAT→GGT)  appY → global transcriptional activator; DLP12 prophage
RA 648,709 A→T 5.1% F288Y (TTC→TAC)  citF ← citrate lyase, citrate‑ACP transferase (alpha) subunit
RA 705,633 G→T 5.0% A564S (GCG→TCG)  nagE → N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components
RA 734,227 C→T 5.1% pseudogene (95/1521 nt) rhsO → pseudogene, Rhs family
RA 755,400 G→A 100% W75* (TGG→TAG)  sdhC → succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA 831,042 G→A 5.6% L57L (CTG→CTA rhlE → ATP‑dependent RNA helicase
RA 832,728 C→T 5.3% A75T (GCA→ACA)  ybiA ← DUF1768 family protein
RA 853,967 G→A 5.5% P107P (CCG→CCA ybiR → putative transporter
RA 872,248 C→T 6.2% T120M (ACG→ATG)  gsiD → glutathione ABC transporter permease
RA 935,464 A→G 11.2% A747A (GCA→GCG ftsK → DNA translocase at septal ring sorting daughter chromsomes
RA 943,269 G→A 5.1% G771S (GGT→AGT)  dmsA → dimethyl sulfoxide reductase, anaerobic, subunit A
RA 961,355 T→G 5.7% V52G (GTT→GGT)  cmk → cytidylate kinase
RA 1,018,388 G→A 5.2% intergenic (‑89/‑97) ycbZ ← / → matP putative peptidase/Ter macrodomain organizer matS‑binding protein
RA 1,114,362 T→C 6.1% R377G (AGA→GGA)  mdtG ← putative drug efflux system protein
RA 1,148,485 T→C 5.4% Y289H (TAT→CAT)  plsX → putative phosphate acyltransferase
RA 1,169,382 C→G 5.3% intergenic (+52/+30) bhsA → / ← ldtC biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein
RA 1,179,260 G→T 5.2% R223M (AGG→ATG)  nagK → N‑acetyl‑D‑glucosamine kinase
RA 1,212,074 T→C 5.5% intergenic (‑71/+629) iraM ← / ← ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
RA 1,221,839 T→C 5.1% pseudogene (2239/2574 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,237,971 A→G 5.5% Q134R (CAG→CGG)  dadA → D‑amino acid dehydrogenase
RA 1,247,144 T→A 5.2% D78V (GAT→GTT)  treA ← periplasmic trehalase
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
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,303,000 T→C 5.2% P34P (CCT→CCC oppB → oligopeptide ABC transporter permease
RA 1,320,243 T→C 5.0% N381S (AAC→AGC)  trpD ← fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase
JC JC 1,335,762 IS5 (–) +4 bp 100% intergenic (+304/‑66) yciX → / → acnA uncharacterized protein/aconitate hydratase 1; aconitase A
RA 1,354,596 C→T 6.6% G292D (GGC→GAC)  sapB ← antimicrobial peptide transport ABC transporter permease
RA 1,381,915 G→T 5.4% intergenic (+13/‑32) ycjV → / → ompG pseudogene; putative ATP‑binding component of a transport system/outer membrane porin G
RA 1,381,918 A→C 5.0% intergenic (+16/‑29) ycjV → / → ompG pseudogene; putative ATP‑binding component of a transport system/outer membrane porin G
RA 1,393,704 G→A 7.5% A160T (GCA→ACA)  mppA → murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA 1,441,265 C→T 6.8% P70S (CCC→TCC)  ydbJ → DUF333 family putative lipoprotein
RA 1,478,995 A→G 5.4% K257R (AAA→AGA)  ynbB → putative CDP‑diglyceride synthase
RA 1,610,455 G→A 7.6% L76L (CTG→TTG)  uxaB ← altronate oxidoreductase, NAD‑dependent
RA 1,626,189 Δ1 bp 6.0% coding (1192/2046 nt) dcp ← dipeptidyl carboxypeptidase II
RA 1,653,241 T→C 8.6% K225K (AAA→AAG rspB ← putative Zn‑dependent NAD(P)‑binding oxidoreductase
RA 1,664,972 T→C 5.4% F156S (TTT→TCT)  dmsD → twin‑argninine leader‑binding protein for DmsA and TorA
RA 1,707,521 G→A 5.8% A201A (GCG→GCA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,714,557 A→T 6.2% T61S (ACT→TCT)  gstA → glutathionine S‑transferase
RA 1,735,899 T→C 7.3% Y174Y (TAT→TAC sodB → superoxide dismutase, Fe
RA 1,744,445 C→T 5.9% A330V (GCC→GTC)  mdtK → multidrug efflux system transporter
RA 1,745,627 C→T 5.6% G167G (GGG→GGA ydhQ ← autotransporter adhesin‑related protein
RA 1,760,053 C→T 6.2% L157L (CTG→CTA sufS ← cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent
RA 1,775,006 C→T 5.2% S107S (AGC→AGT aroD → 3‑dehydroquinate dehydratase
RA 1,798,472 A→G 5.9% T157T (ACT→ACC pheS ← phenylalanine tRNA synthetase, alpha subunit
RA 1,845,554 T→C 6.7% K469K (AAA→AAG topB ← DNA topoisomerase III
RA 1,863,131 Δ1 bp 5.7% coding (361/996 nt) gapA → glyceraldehyde‑3‑phosphate dehydrogenase A
RA 1,864,768 T→C 6.7% intergenic (+34/+14) yeaD → / ← yeaE D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent
RA 1,870,261 G→A 5.8% intergenic (+23/‑124) yeaH → / → yeaI UPF0229 family protein/putative membrane‑anchored diguanylate cyclase
RA 1,903,534 G→A 5.3% V151V (GTG→GTA manY → mannose‑specific enzyme IIC component of PTS
RA 1,959,628 A→G 5.3% N73N (AAT→AAC yecM ← putative metal‑binding enzyme
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 2,025,992 T→A 6.0% F161Y (TTT→TAT)  yedP → putative mannosyl‑3‑phosphoglycerate phosphatase
RA 2,072,813 G→T 5.9% L425L (CTG→CTT flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,092,330 G→A 6.2% A412T (GCC→ACC)  hisD → bifunctional histidinal dehydrogenase/ histidinol dehydrogenase
RA 2,117,903 Δ1 bp 5.9% coding (502/1281 nt) wcaK ← colanic acid biosynthesis protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,160,408 G→A 5.2% E675K (GAA→AAA)  mdtC → multidrug efflux system, subunit C
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 2,219,632 G→A 5.2% intergenic (‑151/+60) osmF ← / ← bglX putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic
RA 2,219,633 C→A 5.3% intergenic (‑152/+59) osmF ← / ← bglX putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic
RA 2,219,646 T→G 6.2% intergenic (‑165/+46) osmF ← / ← bglX putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic
RA 2,219,647 T→C 5.3% intergenic (‑166/+45) osmF ← / ← bglX putative ABC transporter periplasmic binding protein/beta‑D‑glucoside glucohydrolase, periplasmic
RA 2,336,597 T→C 5.0% V16V (GTA→GTG yfaA ← DUF2138 family protein, putative host defense protein
RA 2,396,264 A→C 5.0% C63G (TGT→GGT)  nuoI ← NADH:ubiquinone oxidoreductase, chain I
RA 2,396,553 Δ1 bp 5.1% coding (890/978 nt) nuoH ← NADH:ubiquinone oxidoreductase, membrane subunit H
RA 2,460,614 C→T 5.2% intergenic (‑145/+36) fadI ← / ← yfcZ beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein
RA 2,545,924 C→T 5.3% A51V (GCG→GTG)  murQ → N‑acetylmuramic acid 6‑phosphate (MurNAc‑6‑P) etherase
RA 2,609,899 C→T 5.3% S471S (AGC→AGT hyfG → hydrogenase 4, subunit
RA 2,762,221 G→T 5.1% I440I (ATC→ATA yfjK ← radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage
RA 2,947,466 T→C 9.2% intergenic (+3/‑31) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 3,047,524 C→G 5.2% M506I (ATG→ATC gcvP ← glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex
RA 3,084,171 C→T 5.0% D581N (GAT→AAT)  speA ← biosynthetic arginine decarboxylase, PLP‑binding
RA 3,165,499 C→T 6.1% A159T (GCC→ACC)  parC ← DNA topoisomerase IV, subunit A
RA 3,233,809 G→A 5.7% S112S (AGC→AGT higA ← antitoxinof the HigB‑HigA toxin‑antitoxin system
RA 3,328,182 A→T 5.6% intergenic (+99/+57) yhbY → / ← greA RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA 3,328,183 T→A 5.8% intergenic (+100/+56) yhbY → / ← greA RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor
RA 3,381,705 G→A 6.2% P321P (CCG→CCA degQ → serine endoprotease, periplasmic
RA 3,504,875 T→G 5.0% intergenic (+92/+60) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,504,880 A→T 5.8% intergenic (+97/+55) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,504,882 A→T 5.1% intergenic (+99/+53) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,504,887 C→A 5.0% intergenic (+104/+48) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
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 3,587,412 G→T 5.1% T234T (ACC→ACA ugpQ ← glycerophosphodiester phosphodiesterase, cytosolic
RA 3,781,051 C→G 5.8% intergenic (+34/‑164) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,790,300 A→T 5.8% intergenic (‑219/+20) waaH ← / ← tdh LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
RA 3,790,303 A→T 5.8% intergenic (‑222/+17) waaH ← / ← tdh LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,060,261 G→T 5.2% intergenic (+31/‑186) typA → / → yihL GTP‑binding protein/putative DNA‑binding transcriptional regulator
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 15.5% 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
JC JC 4,545,942 IS1 (+) +9 bp 21.3% coding (847‑855/2637 nt) fimD → fimbrial usher outer membrane porin protein; FimCD chaperone‑usher
RA 4,588,028 A→G 5.2% Y280H (TAC→CAC)  yjiA ← metal‑binding GTPase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 131578 134203 2626 32 [30] [31] 35 [acnB] [acnB]
* * ÷ NC_000913 2066246–2066647 2066647 1–402 32 [30] [31] 32 [insH1] [insH1]
* * ÷ NC_000913 3423721–3424234 3424542–3424238 5–822 32 [31] [31] 32 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 271133NA (NA)3 (0.030) 3/234 NT NA noncoding (593/1221 nt) IS30 repeat region
?NC_000913 = 271141 NA (NA)noncoding (601/1221 nt) IS30 repeat region
* ? NC_000913 274620 =NA (NA)4 (0.050) 4/226 NT NA noncoding (530/1195 nt) IS5 repeat region
?NC_000913 274663 = NA (NA)noncoding (487/1195 nt) IS5 repeat region
* ? NC_000913 = 60104456 (0.620)3 (0.040) 3/226 NT 5.2% coding (2331/3144 nt) cusA copper/silver efflux system, membrane component
?NC_000913 = 601061 57 (0.680)coding (2348/3144 nt) cusA copper/silver efflux system, membrane component
* ? NC_000913 = 758508NA (NA)4 (0.050) 4/230 NT NA noncoding (100/118 nt) RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
?NC_000913 = 758519 NA (NA)noncoding (111/118 nt) RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site
* ? NC_000913 1207790 =45 (0.500)51 (0.650) 42/212 NT 61.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 24 (0.300)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780542 (0.460)32 (0.410) 28/212 NT 51.4% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 24 (0.300)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1839292 =81 (0.890)4 (0.050) 4/234 NT 5.2% coding (546/654 nt) ynjD putative ABC transporter ATPase
?NC_000913 1839333 = 68 (0.780)coding (587/654 nt) ynjD putative ABC transporter ATPase
* ? NC_000913 1966969 =58 (0.640)3 (0.030) 3/236 NT 5.3% coding (69/645 nt) cheZ chemotaxis regulator, protein phosphatase for CheY
?NC_000913 1967014 = 51 (0.580)coding (24/645 nt) cheZ chemotaxis regulator, protein phosphatase for CheY
* ? NC_000913 2169284 =71 (0.780)5 (0.060) 4/228 NT 6.9% coding (573/900 nt) yegS phosphatidylglycerol kinase, metal‑dependent
?NC_000913 2169320 = 69 (0.810)coding (609/900 nt) yegS phosphatidylglycerol kinase, metal‑dependent
* ? NC_000913 2518010 =110 (1.210)4 (0.040)
+GG
4/240 NT 5.0% intergenic (‑178/+31) yfeA/alaX putative diguanylate cyclase/tRNA‑Ala
?NC_000913 2518151 = 44 (0.480)intergenic (‑35/+5) alaX/alaW tRNA‑Ala/tRNA‑Ala
* ? NC_000913 = 258693980 (0.880)4 (0.050) 4/238 NT 5.0% coding (1209/1701 nt) narQ sensory histidine kinase in two‑component regulatory system with NarP
?NC_000913 = 2586950 73 (0.820)coding (1220/1701 nt) narQ sensory histidine kinase in two‑component regulatory system with NarP
* ? NC_000913 3269866 =102 (1.120)4 (0.050) 4/236 NT 5.0% intergenic (+264/+350) yhaC/rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
?NC_000913 3269959 = 53 (0.600)intergenic (+357/+257) yhaC/rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
* ? NC_000913 3654539 =95 (1.050)7 (0.090) 7/220 NT 7.4% intergenic (+12/‑144) slp/dctR outer membrane lipoprotein/Putative LuxR family repressor for dicarboxylate transport
?NC_000913 3654568 = 90 (1.100)intergenic (+41/‑115) slp/dctR outer membrane lipoprotein/Putative LuxR family repressor for dicarboxylate transport
* ? NC_000913 3754811 =NA (NA)3 (0.040) 3/228 NT NA intergenic (‑383/+162) yiaW/aldB DUF3302 family inner membrane protein/aldehyde dehydrogenase B
?NC_000913 3754851 = NA (NA)intergenic (‑423/+122) yiaW/aldB DUF3302 family inner membrane protein/aldehyde dehydrogenase B
* ? NC_000913 = 419982477 (0.850)4 (0.050) 4/234 NT 5.1% coding (321/591 nt) yjaG DUF416 domain protein
?NC_000913 = 4199846 74 (0.850)coding (343/591 nt) yjaG DUF416 domain protein
* ? NC_000913 = 4542690104 (1.150)7 (0.080) 7/226 NT 6.0% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 125 (1.490)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)