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

Predicted mutations
evidence position mutation annotation gene description
RA 24,776 T→C F796L (TTT→CTT)  ileS → isoleucine‑‑tRNA ligase
RA 86,112 A→G L161L (TTA→TTG ilvI → acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit
RA 119,595 C→T A105A (GCC→GCT ampE → protein AmpE
RA 132,519 A→G N302S (AAC→AGC)  acnB → hypothetical protein
RA 164,090 A→G E662E (GAA→GAG hrpB → putative ATP‑dependent RNA helicase HrpB
RA 184,723 G→A A116V (GCC→GTC)  yaeI ← phosphodiesterase YaeI
RA 186,485 G→A A722A (GCC→GCT glnD ← PII uridylyltransferase/uridylyl removing enzyme
RA 218,835 (A)8→7 intergenic (‑60/+52) proS ← / ← trmO proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase
MC JC 257,908 Δ776 bp insB9[crl] insB9, insA9, [crl]
RA 296,675 A→G V141A (GTC→GCC)  intF ← CP4‑6 prophage; putative phage integrase
RA 341,276 A→G D51G (GAC→GGC)  yahJ → putative deaminase with metallo‑dependent hydrolase domain
RA 380,021 (G)10→8 intergenic (‑140/+47) frmR ← / ← yaiO DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
RA 405,536 G→T P37T (CCC→ACC)  proC ← pyrroline‑5‑carboxylate reductase
RA 455,208 A→G T26A (ACC→GCC)  tig → trigger factor
RA 472,742 (G)6→7 coding (145/339 nt) glnK → nitrogen regulator GlnK
RA 485,897 G→A G46D (GGT→GAT)  acrR → DNA‑binding transcriptional repressor AcrR
RA 486,482 C→T intergenic (+74/‑54) acrR → / → mscK DNA‑binding transcriptional repressor AcrR/potassium dependent, small conductance mechanosensitive channel
RA 513,820 A→G L415L (TTA→TTG ybaT → putative transporter YbaT
RA 527,577 T→C intergenic (+36/‑4) rhsD → / → ybbC protein RhsD/PF15631 family protein YbbC
RA 663,851 A→G I38T (ATC→ACC)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase DacA
RA 705,972 (T)9→8 intergenic (+82/‑121) nagE → / → glnS N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase
RA 723,528 (T)8→7 coding (887/2685 nt) kdpD ← sensory histidine kinase KdpD
RA 778,251 T→C V171A (GTT→GCT)  tolB → Tol‑Pal system periplasmic protein TolB
RA 889,923 A→G intergenic (‑104/‑166) ybjL ← / → ybjM putative transport protein YbjL/putative inner membrane protein
RA 915,468 C→T A194T (GCT→ACT)  aqpZ ← water channel AqpZ
RA 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp
RA 936,936 G→C G1238A (GGT→GCT)  ftsK → cell division DNA translocase FtsK
RA 972,000 A→G E83E (GAA→GAG ycbJ → putative phosphotransferase YcbJ
RA 983,040 A→G intergenic (+146/‑35) ldtD → / → ycbK L,D‑transpeptidase LdtD/DUF882 domain‑containing protein YcbK
RA 1,010,898 C→T A312V (GCC→GTC)  uup → ATP‑binding protein with possible role in replication
RA 1,014,334 A→G H359R (CAC→CGC)  pqiB → intermembrane transport protein PqiB
RA 1,097,580 (G)7→8 noncoding (73/88 nt) serX ← tRNA‑Ser
RA 1,109,534 A→G D67G (GAC→GGC)  opgG → osmoregulated periplasmic glucans (OPGs) biosynthesis protein G
RA 1,120,815 A→G G47G (GGT→GGC bssS ← regulator of biofilm formation
RA 1,143,140 T→C T410A (ACT→GCT)  rne ← ribonuclease E
RA 1,195,426 C→T P102S (CCG→TCG)  icd → isocitrate dehydrogenase
RA 1,207,903 T→C W135R (TGG→CGG)  ycfK → e14 prophage; protein StfP
RA 1,220,971 G→A pseudogene (1371/2648 nt) ycgH → putative transporter component, N‑terminal fragment
RA 1,289,331 (A)7→6 coding (87/906 nt) rssA → putative patatin‑like phospholipase RssA
RA 1,328,639 T→C G158G (GGA→GGG yciK ← putative oxidoreductase
RA 1,333,620 G→A G858D (GGC→GAC)  topA → DNA topoisomerase 1
RA 1,399,985 (C)7→8 coding (252/516 nt) ogt ← methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase
RA 1,415,063 T→C D775G (GAC→GGC)  recE ← Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific
RA 1,437,183 T→C noncoding (63/109 nt) micC → small regulatory RNA MicC
RA 1,463,955 A→G A139A (GCA→GCG paaX → DNA‑binding transcriptional repressor PaaX
RA 1,489,590 T→C R453R (CGT→CGC aldA → aldehyde dehydrogenase A
RA 1,491,159 A→G G86G (GGA→GGG cybB → cytochrome b561
RA 1,515,300 A→G Y180C (TAC→TGC)  ydcV → putative ABC transporter membrane subunit YdcV
RA 1,516,041 C→T A155V (GCC→GTC)  patD → gamma‑aminobutyraldehyde dehydrogenase
RA 1,538,930 A→G F1221L (TTC→CTC)  narZ ← nitrate reductase Z subunit alpha
RA 1,541,351 C→T E414K (GAA→AAA)  narZ ← nitrate reductase Z subunit alpha
RA 1,566,171 C→T G324S (GGT→AGT)  dosC ← diguanylate cyclase DosC
RA 1,594,132 (C)8→9 pseudogene (3955/5422 nt) yneO ← AIDA‑I family autotransporter YneO
RA 1,634,642 C→T G82S (GGC→AGC)  tfaQ ← Qin prophage; putative tail fiber assembly protein TfaQ
RA 1,683,424 A→G E181E (GAA→GAG rstB → sensory histidine kinase RstB
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarase C
RA 1,731,215 A→G H710R (CAT→CGT)  lhr → putative ATP‑dependent helicase Lhr
RA 1,825,986 C→T R313H (CGC→CAC)  astE ← succinylglutamate desuccinylase
RA 1,833,212 T→C V262A (GTC→GCC)  xthA → exodeoxyribonuclease III
RA 1,873,384 A→G K448K (AAA→AAG dgcJ → putative diguanylate cyclase DgcJ
RA 1,875,056 (C)6→7 coding (521/822 nt) nimR ← DNA‑binding transcriptional repressor NimR
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
MC JC 1,978,503 Δ776 bp insB‑5insA‑5 insB‑5, insA‑5
RA 2,049,679 T→C L1581P (CTG→CCG)  yeeJ → inverse autotransporter adhesin
RA 2,117,185 T→C E407G (GAG→GGG)  wcaK ← putative colanic acid biosynthesis pyruvyl transferase
RA 2,129,520 T→C N44S (AAC→AGC)  wcaE ← putative colanic acid biosynthesis glycosyl transferase
RA 2,168,165 T→C T48A (ACC→GCC)  yegR ← uncharacterized protein YegR
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,184,736 C→G G189A (GGT→GCT)  thiM ← hydroxyethylthiazole kinase
RA 2,197,918 T→C intergenic (+620/‑2361) yehF → / → yehI putative protein YehF/DUF4132 domain‑containing protein YehI
RA 2,206,031 G→A D113N (GAT→AAT)  yehM → putative YehN
RA 2,286,291 (A)5→4 intergenic (+4/+99) proL → / ← yejO tRNA‑Pro/adhesin‑like autotransporter YejO
RA 2,325,984 T→C I410T (ATC→ACC)  atoE → short chain fatty acid transporter
RA 2,446,579 T→C T299A (ACC→GCC)  aroC ← chorismate synthase
RA 2,477,624 T→C E2E (GAA→GAG dsdC ← DNA‑binding transcriptional dual regulator DsdC
RA 2,480,487 T→C V429A (GTG→GCG)  dsdA → D‑serine ammonia‑lyase
RA 2,511,445 T→C intergenic (+118/+23) ypeC → / ← mntH DUF2502 domain‑containing protein YpeC/Mn(2(+))/Fe(2(+)): H(+) symporter MntH
RA 2,526,738 T→C E40G (GAA→GGA)  yfeR ← putative LysR‑type DNA‑binding transcriptional regulator YfeR
RA 2,527,823 T→C V293A (GTG→GCG)  yfeH → putative solute:Na(+) symporter
RA 2,575,000 (T)6→5 coding (4/702 nt)
coding (458/480 nt)
eutQ ←
eutP ←
putative ethanolamine utilization protein EutQ
putative ethanolamine utilization protein EutP with nucleoside triphosphate hydrolase domain
RA 2,586,334 A→G T202A (ACC→GCC)  narQ → sensory histidine kinase NarQ
RA 2,608,676 T→C F64L (TTT→CTT)  hyfG → hydrogenase 4 catalytic subunit HyfG
RA 2,631,085 T→C H484R (CAC→CGC)  guaA ← GMP synthetase
RA 2,638,026 (C)6→7 coding (627/1179 nt) bamB ← outer membrane protein assembly factor BamB
RA 2,657,686 A→G V417A (GTG→GCG)  hscA ← iron‑sulfur cluster biosynthesis chaperone HscA
RA 2,686,857 T→C G341G (GGT→GGC hmp → nitric oxide dioxygenase
RA 2,785,204 (A)8→7 intergenic (‑193/+558) ypjC ← / ← ileY DUF5507 domain‑containing protein YpjC/tRNA‑Ile
RA 2,811,134 A→G H122R (CAC→CGC)  mprA → DNA‑binding transcriptional repressor MprA
RA 2,814,290 T→C E148E (GAA→GAG luxS ← S‑ribosylhomocysteine lyase
RA 2,816,416 C→T A8A (GCG→GCA gshA ← glutamate‑‑cysteine ligase
RA 2,826,722 G→A G111S (GGC→AGC)  srlE → sorbitol‑specific PTS enzyme IIBC1 component
RA 2,855,509 T→C V391A (GTG→GCG)  fhlA → DNA‑binding transcriptional activator FhlA
MC JC 2,857,096 Δ2,538 bp coding (4‑2541/2562 nt) mutS → DNA mismatch repair protein MutS
RA 2,949,993 (T)5→6 coding (752/1332 nt) argA → N‑acetylglutamate synthase
RA 2,955,650 T→C E118E (GAA→GAG recB ← exodeoxyribonuclease V subunit RecB
RA 2,964,144 T→C T12A (ACG→GCG)  ppdA ← conserved protein PpdA
RA 3,020,895 T→C V119A (GTC→GCC)  ygfM → putative oxidoreductase
RA 3,063,906 T→C V307A (GTC→GCC)  argK → methylmalonyl‑CoA mutase‑interacting GTPase YgfD
RA 3,068,157 T→C intergenic (‑77/+16) yggE ← / ← argO uncharacterized protein YggE/L‑arginine exporter
RA 3,073,784 T→C intergenic (‑93/+192) epd ← / ← yggC D‑erythrose‑4‑phosphate dehydrogenase/P‑loop NTPase domain‑containing protein YggC
RA 3,094,703 (C)5→4 coding (378/981 nt) yggR ← Type II/IV secretion system family protein
RA 3,146,132 T→C T44A (ACT→GCT)  hybO ← hydrogenase 2 small subunit
RA 3,197,632 A→G G670G (GGT→GGC glnE ← fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase
RA 3,255,685 A→G C323R (TGT→CGT)  cyuA ← putative L‑cysteine desulfidase CyuA
RA 3,257,356 (T)5→4 coding (655/1332 nt) cyuP ← putative D/L‑serine transporter
RA 3,348,279 (C)6→7 intergenic (+41/‑173) npr → / → yrbL phosphorelay protein Npr/protein kinase‑like domain‑containing protein YrbL
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,388,726 A→G V134A (GTT→GCT)  aaeA ← aromatic carboxylic acid efflux pump membrane fusion protein
RA 3,448,581 T→C K60R (AAG→AGG)  rpmC ← 50S ribosomal subunit protein L29
RA 3,517,260 T→A D16V (GAT→GTT)  damX ← cell division protein DamX
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,649,516 A→G L194L (TTA→TTG arsB → arsenite/antimonite:H(+) antiporter
RA 3,690,933 G→A P559S (CCT→TCT)  bcsB ← cellulose synthase periplasmic subunit
RA 3,696,493 T→C G12G (GGT→GGC bcsE → c‑di‑GMP‑binding protein BcsE
RA 3,755,238 G→A A425V (GCG→GTG)  aldB ← aldehyde dehydrogenase B
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,836,468 T→C intergenic (+152/‑485) selC → / → setC tRNA‑Sec/putative arabinose exporter
RA 3,847,201 A→G intergenic (‑34/+104) uhpT ← / ← uhpC hexose‑6‑phosphate:phosphate antiporter/inner membrane protein sensing glucose‑6‑phosphate
RA 3,853,966 A→G L15L (TTA→TTG emrD → multidrug efflux pump EmrD
RA 3,860,630 (C)5→4 coding (348/894 nt) yidL → putative DNA‑binding transcriptional regulator YidL
RA 3,926,259 A→G L66P (CTT→CCT)  mioC ← flavoprotein MioC
RA 3,935,073 (A)6→5 coding (1296/1506 nt) rbsA → ribose ABC transporter ATP binding subunit
RA 3,994,558 A→G T13A (ACT→GCT)  yifL → putative lipoprotein YifL
RA 4,011,856 A→G T261A (ACG→GCG)  bioP → biotin transporter
RA 4,032,131 T→C V324A (GTC→GCC)  pepQ → Xaa‑Pro dipeptidase
RA 4,075,441 A→G Q258R (CAG→CGG)  yihW → putative DNA‑binding transcriptional regulator YihW
RA 4,124,105 A→G L118L (TTG→CTG)  cytR ← DNA‑binding transcriptional repressor CytR
RA 4,185,871 C→T D174D (GAC→GAT rpoC → RNA polymerase subunit beta'
RA 4,188,352 G→A A1001A (GCG→GCA rpoC → RNA polymerase subunit beta'
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,440,531 C→T E229K (GAA→AAA)  ytfL ← putative inner membrane protein
RA 4,442,332 C→T intergenic (‑156/‑50) msrA ← / → tamA methionine sulfoxide reductase A/translocation and assembly module subunit TamA
RA 4,445,549 A→G T480A (ACC→GCC)  tamB → translocation and assembly module subunit TamB
RA 4,487,894 G→A A193T (GCT→ACT)  lptG → lipopolysaccharide transport system protein LptG
RA 4,514,021 G→A A96A (GCC→GCT fecB ← ferric citrate ABC transporter periplasmic binding protein
RA 4,572,630 (T)6→7 coding (217/1518 nt) yjiT → putative uncharacterized protein YjiT
RA 4,606,094 (G)8→7 noncoding (72/87 nt) leuV ← tRNA‑Leu
JC 4,606,330 (G)8→11 noncoding (72/87 nt) leuQ ← tRNA‑Leu
RA 4,610,149 T→C F246L (TTC→CTC)  prfC → peptide chain release factor RF3

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 270648–271294 271484–271385 92–837 14 [13] [12] 14 insI‑1 IS30 transposase
* * ÷ NC_000913 3423777–3424234 3424527–3424239 6–751 15 [13] [13] 14 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3762360–3764072 3765194–3764077 6–2835 14 [11] [13] 14 rhsA rhs element protein RhsA
* * ÷ NC_000913 3765317–3765410 3765545–3765414 5–229 15 [12] [13] 17 rhsA rhs element protein RhsA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 374921 =NA (NA)23 (0.630) 16/190 1.1 NA intergenic (+40/‑538) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377531 = NA (NA)intergenic (+220/+4) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 374922 =NA (NA)11 (0.280) 9/202 2.6 NA intergenic (+41/‑537) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377430 = NA (NA)intergenic (+119/+105) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 = 374963NA (NA)24 (0.650) 17/190 1.0 NA noncoding (33/34 nt) other REP31a
?NC_000913 = 377487 NA (NA)intergenic (+176/+48) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 375124 =NA (NA)10 (0.270) 7/192 3.0 NA intergenic (+243/‑335) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377530 = NA (NA)intergenic (+219/+5) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 375327 =NA (NA)20 (0.390) 13/262 2.5 NA intergenic (+446/‑132) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377328 = NA (NA)intergenic (+17/+207) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 1207790 =9 (0.170)55 (1.160) 39/244 0.2 87.3% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 8 (0.170)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12078059 (0.170)26 (0.550) 22/244 1.1 76.5% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 8 (0.170)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)69 (1.330) 47/268 0.1 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 3363001 =81 (1.510)85 (1.600) 53/274 0.1 67.3% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 2 (0.040)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)67 (1.250) 47/276 0.1 94.4% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 4 (0.070)coding (3907/4134 nt) rhsA rhs element protein RhsA