breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 99,678 C→T 5.2% A12V (GCA→GTA)  murG → N‑acetylglucosaminyl transferase
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 262,225 G→T 8.7% V241V (GTG→GTT proA → gamma‑glutamylphosphate reductase
RA 349,717 T→C 6.2% intergenic (+145/‑295) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 606,958 Δ1 bp 5.1% coding (426/1119 nt) ybdK ← weak gamma‑glutamyl:cysteine ligase
RA 734,791 A→G 5.3% pseudogene (659/1521 nt) rhsO → pseudogene, Rhs family
RA 759,007 T→G 13.8% F101C (TTC→TGC)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 867,917 T→C 6.4% L133P (CTG→CCG)  gsiA → glutathione ABC transporter ATPase
RA 1,039,722 C→T 6.1% L143F (CTC→TTC)  cbdB → cytochrome bd‑II oxidase, subunit II
RA 1,054,863 T→C 5.1% K439R (AAA→AGA)  torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,073,852 G→A 5.2% Q54* (CAA→TAA)  rutA ← pyrimidine oxygenase, FMN‑dependent
RA 1,261,297 G→T 100% D193E (GAC→GAA prs ← phosphoribosylpyrophosphate synthase
RA 1,261,471 A→C 8.8% I135M (ATT→ATG prs ← phosphoribosylpyrophosphate synthase
RA 1,287,152 T→C 6.5% noncoding (85/171 nt)
T9A (ACT→GCT) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
JC JC 1,293,015 IS1 (+) +8 bp 5.1% intergenic (‑93/‑505) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC 1,293,091 IS1 (+) +9 bp 12.4% intergenic (‑169/‑428) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
JC JC 1,351,197 IS186 (–) +6 bp :: Δ1 bp 75.0% intergenic (‑158/+205) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA 1,380,351 G→A 6.0% S68S (TCG→TCA ycjU → beta‑phosphoglucomutase
RA 1,448,094 Δ1 bp 5.4% coding (576/1500 nt) feaB → phenylacetaldehyde dehydrogenase
RA 1,466,055 G→T 5.5% pseudogene (664/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,508,007 T→A 5.2% R409R (CGT→CGA ydcP → putative peptidase
RA 1,525,331 T→C 5.6% H217R (CAC→CGC)  ansP ← L‑asparagine transporter
RA 1,557,347 A→G 5.9% L231P (CTG→CCG)  ddpF ← D,D‑dipeptide ABC transporter ATPase
RA 1,708,930 C→A 24.1% P671Q (CCG→CAG)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
JC JC 1,757,082 IS5 (–) +4 bp 26.2% coding (1385‑1388/1413 nt) pykF → pyruvate kinase I
JC JC 1,757,082 IS5 (+) +4 bp 64.7% coding (1385‑1388/1413 nt) pykF → pyruvate kinase I
RA 1,759,548 A→G 5.9% Y326H (TAT→CAT)  sufS ← cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent
RA 1,797,774 C→T 6.8% P57P (CCG→CCA pheT ← phenylalanine tRNA synthetase, beta subunit
RA 1,816,983 A→G 5.3% R51R (CGT→CGC chbG ← chito‑oligosaccharide deacetylase
RA 1,974,817 C→G 5.1% G170R (GGG→CGG)  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 2,019,460 G→A 100% V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
RA 2,047,453 C→T 5.0% T839I (ACT→ATT)  yeeJ → putative adhesin
RA 2,072,013 C→T 5.4% H159Y (CAT→TAT)  flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,072,491 C→T 5.4% T318M (ACG→ATG)  flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,076,294 A→G 5.2% K506E (AAA→GAA)  yeeR → CP4‑44 prophage; putative membrane protein
RA 2,126,158 A→T 5.0% F22Y (TTT→TAT)  wcaH ← GDP‑mannose mannosyl hydrolase
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 2,250,988 A→T 5.1% D50V (GAT→GTT)  nfo → endonuclease IV with intrinsic 3'‑5' exonuclease activity
RA 2,263,235 C→T 6.9% W87* (TGG→TGA) ‡ fruB ← fused fructose‑specific PTS enzymes: IIA component/HPr component
RA 2,263,236 C→G 7.9% W87S (TGG→TCG) ‡ fruB ← fused fructose‑specific PTS enzymes: IIA component/HPr component
RA 2,263,237 A→G 5.8% W87R (TGG→CGG) ‡ fruB ← fused fructose‑specific PTS enzymes: IIA component/HPr component
RA 2,304,649 C→T 11.8% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,317,667 T→G 100% E737A (GAA→GCA)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,367,945 G→T 16.1% G292V (GGT→GTT)  arnC → undecaprenyl phosphate‑L‑Ara4FN transferase
RA 2,550,064 T→C 5.5% K161R (AAA→AGA)  yfeX ← porphyrinogen oxidase, cytoplasmic
RA 2,560,985 C→A 17.4% intergenic (+87/‑383) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,569,416 G→A 5.2% C32C (TGC→TGT eutG ← ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase
RA 2,632,046 G→T 100% P164T (CCG→ACG)  guaA ← GMP synthetase (glutamine aminotransferase)
RA 2,707,923 G→A 5.8% R278C (CGC→TGC)  rseB ← anti‑sigma E factor, binds RseA
JC JC 2,867,796 IS1 (+) +9 bp 22.9% coding (950‑958/1140 nt) nlpD ← activator of AmiC murein hydrolase activity, lipoprotein
RA 2,969,920 G→T 5.4% G87C (GGT→TGT)  mutH → methyl‑directed mismatch repair protein
RA 2,975,601 T→G 5.2% E138D (GAA→GAC aas ← fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase
RA 3,002,530 G→A 100% G729D (GGT→GAT)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
RA 3,056,551 T→A 6.4% V104E (GTG→GAG)  fau → 5‑formyltetrahydrofolate cyclo‑ligase family protein
RA 3,231,792 T→C 6.4% F43S (TTT→TCT)  fadH → 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA 3,269,917 T→C 7.0% intergenic (+315/+299) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,194 G→T 6.8% intergenic (+592/+22) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,195 A→C 10.1% intergenic (+593/+21) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,270,196 A→G 7.1% intergenic (+594/+20) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,391,321 G→C 6.4% V236V (GTC→GTG tldD ← putative peptidase
RA 3,485,594 G→A 5.0% R75R (CGC→CGT yhfA ← OsmC 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 3,608,695 C→G 6.6% intergenic (+46/+56) zntA → / ← tusA zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase
RA 3,608,701 A→C 6.0% intergenic (+52/+50) zntA → / ← tusA zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase
JC JC 3,890,075 IS5 (–) +4 bp 100% coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,936,278 A→G 5.5% M1M (ATG→GTG) † rbsB → D‑ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor
RA 3,954,662 C→T 5.1% C395C (TGC→TGT ilvD → dihydroxyacid dehydratase
RA 3,998,273 G→A 5.5% L97L (TTG→TTA uvrD → DNA‑dependent ATPase I and helicase II
RA 4,296,060 C→T 37.9% 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 4,305,438 G→A 5.3% A387V (GCG→GTG)  yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,628,195 A→G 49.5% Y294C (TAC→TGC)  nadR → trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423739–3424234 3424607–3424239 6–869 39 [35] [37] 39 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3514373 3515114 742 38 [35] [37] 39 [gph]–[dam] [gph],rpe,[dam]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 223995NA (NA)3 (0.030) 3/256 NT NA noncoding (225/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
?NC_000913 = 224006 NA (NA)noncoding (236/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
* ? NC_000913 = 225530NA (NA)3 (0.030) 3/256 NT NA noncoding (31/76 nt) alaV tRNA‑Ala
?NC_000913 = 225537 NA (NA)noncoding (38/76 nt) alaV tRNA‑Ala
* ? NC_000913 = 53354786 (0.950)4 (0.050) 3/230 NT 5.1% coding (537/816 nt) allR glyoxylate‑inducible transcriptional repressor of all and gcl operons
?NC_000913 = 533529 75 (0.960)coding (519/816 nt) allR glyoxylate‑inducible transcriptional repressor of all and gcl operons
* ? NC_000913 = 109746314 (0.150)4 (0.050) 5/250 NT 22.8% intergenic (+634/+102) ycdU/serX putative inner membrane protein/tRNA‑Ser
?NC_000913 = 1097467 14 (0.160)intergenic (+638/+98) ycdU/serX putative inner membrane protein/tRNA‑Ser
* ? NC_000913 1207790 =25 (0.280)35 (0.440) 34/234 NT 57.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 30 (0.380)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780525 (0.280)39 (0.490) 34/234 NT 60.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 30 (0.380)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)102 (1.160) 77/258 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 1411899 =113 (1.250)6 (0.080) 6/214 NT 7.1% coding (50/936 nt) ttcA tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
?NC_000913 = 1434958 67 (0.920)pseudogene (51/51 nt) ttcC pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
* ? NC_000913 = 194699757 (0.630)3 (0.030) 3/254 NT 5.2% coding (380/522 nt) ruvC component of RuvABC resolvasome, endonuclease
?NC_000913 = 1947009 55 (0.640)coding (368/522 nt) ruvC component of RuvABC resolvasome, endonuclease
* ? NC_000913 4542682 =102 (1.120)11 (0.130) 10/248 NT 8.9% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 129 (1.530)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 4542690102 (1.120)12 (0.140) 10/248 NT 9.7% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 129 (1.530)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)