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 197,248 G→A 6.2% A235T (GCA→ACA)  rseP → inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease
RA 222,958 Δ1 bp 100% coding (126/576 nt) gmhB → D,D‑heptose 1,7‑bisphosphate phosphatase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 305,971 C→T 5.2% A283T (GCC→ACC)  ecpD ← polymerized tip adhesin of ECP fibers
RA 331,406 C→A 7.5% T648T (ACC→ACA betT → choline transporter of high affinity
RA 531,546 C→A 5.8% E226* (GAA→TAA)  allS ← allD operon transcriptional activator
RA 566,173 C→G 14.0% pseudogene (204/279 nt) exoD ← pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related
RA 566,205 T→C 12.1% pseudogene (172/279 nt) exoD ← pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related
RA 566,245 G→A 8.9% pseudogene (132/279 nt) exoD ← pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related
RA 574,295 G→T 6.7% D114Y (GAT→TAT)  quuD → DLP12 prophage; putative antitermination protein
RA 581,133 A→G 8.8% K100K (AAA→AAG nohD → DLP12 prophage; DNA packaging protein
RA 581,185 C→T 10.9% L118L (CTG→TTG)  nohD → DLP12 prophage; DNA packaging protein
RA 581,227 A→C 22.4% I132L (ATC→CTC)  nohD → DLP12 prophage; DNA packaging protein
RA 737,043 T→C 5.6% pseudogene (219/1137 nt) ybfL → pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA 737,928 C→G 6.4% pseudogene (1104/1137 nt) ybfL → pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA 805,325 T→C 5.7% V608A (GTG→GCG)  ybhJ → aconitase family protein
RA 915,213 A→T 16.7% intergenic (‑356/+139) ybjE ← / ← aqpZ putative transporter/aquaporin Z
RA 915,226 T→G 11.8% intergenic (‑369/+126) ybjE ← / ← aqpZ putative transporter/aquaporin Z
RA 1,049,827 T→G 5.3% intergenic (‑83/‑6) gfcA ← / → insA O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
RA 1,086,485 G→T 6.2% P12Q (CCA→CAA)  pgaD ← biofilm PGA synthase PgaCD, regulatory subunit; c‑di‑GMP‑stimulated activity and dimerization
RA 1,092,203 C→T 5.1% A29A (GCG→GCA pgaA ← biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA 1,113,077 C→A 5.6% R739S (CGT→AGT)  opgH → OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist
RA 1,120,913 C→A 6.3% G15W (GGG→TGG)  bssS ← biofilm regulator
RA 1,269,897 T→G 8.8% noncoding (40/66 nt) rdlB → sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB
RA 1,386,010 C→A 6.1% S167* (TCG→TAG)  ycjF → UPF0283 family inner membrane protein
RA 1,402,454 G→T 5.5% Q268K (CAG→AAG)  abgB ← p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA 1,405,953 C→T 10.2% intergenic (‑202/‑26) mcaS ← / → smrA motility and biofilm regulator sRNA/DNA endonuclease
RA 1,411,384 C→T 10.5% A189T (GCC→ACC)  ttcA ← tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
RA 1,451,132 G→T 7.5% P73H (CCT→CAT)  tynA ← tyramine oxidase, copper‑requiring
RA 1,476,962 T→C 6.6% W607R (TGG→CGG)  ydbD → PF10971 family putative periplasmic methylglyoxal resistance protein
RA 1,498,458 T→C 5.1% F535L (TTC→CTC)  opgD → OPG biosynthetic periplasmic protein
RA 1,517,534 C→A 6.0% P49Q (CCG→CAG)  ydcX → DUF2566 family protein
RA 1,571,296 C→A 6.7% L250L (CTG→CTT gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,610,940 G→T 7.9% T305T (ACC→ACA yneF ← putative membrane‑bound diguanylate cyclase
RA 1,635,293 G→A 7.5% T185T (ACC→ACT stfQ ← Qin prophage; putative side tail fibre assembly protein
RA 1,635,296 T→G 7.5% G184G (GGA→GGC stfQ ← Qin prophage; putative side tail fibre assembly protein
RA 1,635,322 C→T 5.6% E176K (GAA→AAA)  stfQ ← Qin prophage; putative side tail fibre assembly protein
RA 1,689,399 C→T 6.4% A275V (GCG→GTG)  manA → mannose‑6‑phosphate isomerase
RA 1,689,815 G→T 5.5% intergenic (+64/‑37) manA → / → ydgA mannose‑6‑phosphate isomerase/DUF945 family protein
RA 1,782,761 C→A 7.2% I27I (ATC→ATA ydiT → putative 3Fe‑4S ferredoxin‑type protein
RA 1,919,279 A→G 11.6% V590V (GTA→GTG yebT → MCE domain protein
RA 1,941,612 G→T 5.3% V8V (GTC→GTA mepM ← murein DD‑endopeptidase, space‑maker hydrolase, septation protein
RA 1,975,135 C→A 5.7% E64* (GAA→TAA)  cheA ← fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
RA 2,013,898 G→T 5.5% G224W (GGG→TGG)  fliF → flagellar basal‑body MS‑ring and collar protein
RA 2,019,460 G→A 100% V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
RA 2,046,785 G→T 5.7% V616V (GTG→GTT yeeJ → putative adhesin
RA 2,132,403 G→T 6.3% I51I (ATC→ATA wcaB ← putative acyl transferase
RA 2,147,021 T→C 94.6% M174V (ATG→GTG)  alkA ← 3‑methyl‑adenine DNA glycosylase II
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 2,257,293 C→G 5.0% A15P (GCA→CCA)  psuT ← putative nucleoside transporter
RA 2,259,286 T→C 5.1% K4R (AAG→AGG)  psuK ← pseudouridine kinase
RA 2,297,107:1 +C 100% coding (538/624 nt) ccmA ← heme export ABC transporter ATPase
RA 2,312,239 G→T 6.5% Q171K (CAG→AAG)  ompC ← outer membrane porin protein C
JC JC 2,375,828 IS186 (+) +4 bp 100% coding (132‑135/963 nt) menC ← O‑succinylbenzoyl‑CoA synthase
RA 2,753,308 T→C 6.9% V505A (GTC→GCC)  recN → recombination and repair protein
RA 2,818,324 G→A 6.1% intergenic (‑50/+149) argY ← / ← argV tRNA‑Arg/tRNA‑Arg
RA 2,818,331 G→T 5.9% intergenic (‑57/+142) argY ← / ← argV tRNA‑Arg/tRNA‑Arg
RA 2,821,424 G→C 88.3% G196G (GGC→GGG alaS ← alanyl‑tRNA synthetase
RA 2,826,080 G→T 5.0% M83I (ATG→ATT srlA → glucitol/sorbitol‑specific enzyme IIC component of PTS
RA 2,859,142 G→A 90.1% A684T (GCC→ACC)  mutS → methyl‑directed mismatch repair protein
RA 2,904,212 G→A 100% intergenic (+838/+535) ygcE → / ← queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
RA 2,984,895 G→T 5.1% P233H (CCT→CAT)  yqeF ← short chain acyltransferase
RA 3,068,506 G→T 6.7% A101A (GCC→GCA argO ← arginine transporter
RA 3,116,386 C→A 5.2% A909A (GCG→GCT sslE ← putative secreted and surface‑associated lipoprotein mucinase
RA 3,150,525 C→T 5.6% C288C (TGC→TGT yghA → putative oxidoreductase
RA 3,299,293 C→A 5.2% P107Q (CCG→CAG)  yhbO → stress‑resistance protein
RA 3,423,531 T→G 6.6% noncoding (12/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,423,540 A→G 8.7% noncoding (3/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,449,937 G→T 6.4% R99R (CGC→CGA rplV ← 50S ribosomal subunit protein L22
RA 3,449,960 G→T 6.2% R92S (CGT→AGT)  rplV ← 50S ribosomal subunit protein L22
RA 3,449,971 C→T 6.8% R88H (CGT→CAT)  rplV ← 50S ribosomal subunit protein L22
RA 3,504,861 T→A 15.6% intergenic (+78/+74) 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 3,577,360 C→T 8.2% R78H (CGC→CAC)  gntK ← gluconate kinase 2
RA 3,635,235 T→G 5.1% L132R (CTG→CGG)  yhiM → acid resistance protein, inner membrane
RA 3,859,354 T→C 48.7% N255D (AAC→GAC)  yidK ← putative transporter
JC JC 3,890,075 IS5 (–) +4 bp 100% coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,894,980 C→A 7.8% P110Q (CCG→CAG)  chrR → chromate reductase, Class I, flavoprotein
RA 3,903,621 G→A 18.5% G27G (GGC→GGT bglB ← cryptic phospho‑beta‑glucosidase B
RA 3,907,574 T→C 6.9% D2G (GAC→GGC)  phoU ← negative regulator of PhoR/PhoB two‑component regulator
RA 3,909,566 G→A 6.0% A278V (GCG→GTG)  pstC ← phosphate ABC transporter permease
RA 3,936,327 C→T 7.1% A17V (GCC→GTC)  rbsB → D‑ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor
RA 4,105,496 C→A 6.4% G59C (GGT→TGT)  cpxR ← response regulator in two‑component regulatory system with CpxA
RA 4,171,648 A→C 5.7% noncoding (12/120 nt) rrfB → 5S ribosomal RNA of rrnB operon
RA 4,186,578 A→G 89.3% D410G (GAT→GGT)  rpoC → RNA polymerase, beta prime subunit
RA 4,213,390 C→T 5.6% Q53* (CAA→TAA)  yjaA → stress‑induced protein
RA 4,285,364 T→C 12.4% intergenic (‑151/+49) yjcH ← / ← acs DUF485 family inner membrane protein/acetyl‑CoA synthetase
RA 4,296,060 C→T 22.1% 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
RA 4,304,455 C→A 6.4% intergenic (‑52/+157) ytcA ← / ← yjcS putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein
RA 4,329,852 C→A 5.2% P165T (CCT→ACT)  yjcZ → YjcZ family protein; yhjH motility defect suppressor
RA 4,385,382 C→A 5.5% intergenic (+41/‑11) yjeM → / → yjeN putative transporter/uncharacterized protein
RA 4,406,129 T→C 92.5% intergenic (+144/‑61) purA → / → nsrR adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon
RA 4,407,134 G→T 5.6% G161C (GGC→TGC)  rnr → exoribonuclease R, RNase R
RA 4,411,493 C→T 5.3% G64G (GGC→GGT yjfK → DUF2491 family protein
RA 4,538,900 G→A 5.2% T201M (ACG→ATG)  nanC ← N‑acetylnuraminic acid outer membrane channel protein
RA 4,550,253 C→T 5.1% V348V (GTG→GTA gntP ← fructuronate transporter
RA 4,606,207:1 +G 100% noncoding (80/87 nt) leuP ← tRNA‑Leu
RA 4,633,657 C→T 100% C30Y (TGC→TAC)  yjjX ← non‑canonical purine NTP phosphatase, ITPase/XTPase
RA 4,633,785 C→A 7.0% intergenic (‑40/‑12) yjjX ← / → ytjC non‑canonical purine NTP phosphatase, ITPase/XTPase/phosphatase
RA 4,634,087 C→A 8.8% T97T (ACC→ACA ytjC → phosphatase
JC JC 4,640,551 IS1 (–) +9 bp 100% intergenic (+9/‑383) yjjY → / → yjtD uncharacterized protein/putative methyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 366172 366389 218 27 [21] [23] 28 [lacZ] [lacZ]
* * ÷ NC_000913 773026 774179 1154 24 [22] [22] 25 [cydA]–[cydB] [cydA],[cydB]
* * ÷ NC_000913 1037711 1039292 1582 24 [22] [21] 26 cbdA cbdA
* * ÷ NC_000913 1166027 1167400 1374 24 [22] [21] 25 ndh ndh
* * ÷ NC_000913 3423770–3424234 3424525–3424238 5–756 27 [21] [20] 27 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 290634 =NA (NA)4 (0.040) 4/256 NT NA noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 3470951 NA (NA)coding (379/1185 nt) tufA translation elongation factor EF‑Tu 1
* ? NC_000913 374922 =NA (NA)13 (0.140) 5/240 NT NA intergenic (+41/‑537) mhpE/mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
?NC_000913 377329 = NA (NA)intergenic (+18/+206) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 374922 =NA (NA)6 (0.060)
+GCCA
4/248 NT 6.2% intergenic (+41/‑537) mhpE/mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
?NC_000913 = 758445 93 (0.910)noncoding (37/118 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 = 37492983 (1.110)12 (0.180) 7/170 NT 13.8% intergenic (+48/‑530) mhpE/mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
?NC_000913 = 377521 NA (NA)noncoding (187/187 nt) REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
* ? NC_000913 374930 =NA (NA)35 (0.520) 7/170 NT 33.2% noncoding (1/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 377522 = 78 (1.040)intergenic (+211/+13) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 375124 =115 (1.130)5 (0.070) 3/172 NT 6.1% noncoding (195/436 nt) REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
?NC_000913 377530 = 77 (1.130)intergenic (+219/+5) yaiL/frmB DUF2058 family protein/S‑formylglutathione hydrolase
* ? NC_000913 566098 =92 (0.900)8 (0.090)
+GAGAGGAGGATTACAAA
7/222 NT 7.8% pseudogene (279/279 nt) exoD pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related
?NC_000913 4397412 = 126 (1.240)coding (1/1848 nt) mutL methyl‑directed mismatch repair protein
* ? NC_000913 608011 =NA (NA)9 (0.090) 6/248 NT NA noncoding (5/1345 nt) IS186 repeat region
?NC_000913 = 2515625 NA (NA)intergenic (+182/+18) insL1/yfeA IS186 transposase/putative diguanylate cyclase
* ? NC_000913 = 78101653 (0.520)3 (0.030) 3/220 NT 5.7% intergenic (+98/‑52) lysW/valZ tRNA‑Lys/tRNA‑Val
?NC_000913 781653 = 53 (0.610)intergenic (+1/‑432) lysQ/nadA tRNA‑Lys/quinolinate synthase, subunit A
* ? NC_000913 1207790 =38 (0.370)31 (0.350) 20/224 NT 47.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 36 (0.400)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780539 (0.380)33 (0.370) 16/224 NT 48.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 36 (0.400)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)74 (0.750) 40/248 NT 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 4373286 =78 (0.950)55 (0.670) 6/206 NT 41.4% noncoding (90/99 nt) RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
?NC_000913 4374508 = NA (NA)noncoding (11/99 nt) RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
* ? NC_000913 4373296 =69 (0.730)95 (1.010) 7/236 NT 58.1% intergenic (+134/+69) yjeI/yjeJ DUF4156 family lipoprotein/uncharacterized protein
?NC_000913 4374498 = NA (NA)noncoding (1/99 nt) RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site