mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 43,291 | T→C | V35A (GTC→GCC) | fixB → | putative electron transfer flavoprotein FixB |
| RA | 180,119 | T→C | L295L (TTG→CTG) | dgt → | dGTP triphosphohydrolase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 310,450 | A→G | A74A (GCT→GCC) | ecpA ← | common pilus major subunit |
| RA | 349,031 | A→G | Q117R (CAG→CGG) | prpB → | 2‑methylisocitrate lyase |
| RA | 349,192 | A→G | I171V (ATC→GTC) | prpB → | 2‑methylisocitrate lyase |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 382,567 | T→C | C298C (TGT→TGC) | insD‑1 → | IS2 element protein |
| RA | 386,908 | A→G | P234P (CCA→CCG) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 485,225 | A→G | L132P (CTG→CCG) | acrA ← | multidrug efflux pump membrane fusion lipoprotein AcrA |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 607,055 | A→G | V110A (GTA→GCA) | ybdK ← | carboxylate‑amine ligase |
| RA | 648,135 | A→G | G479G (GGT→GGC) | citF ← | citrate lyase alpha subunit |
| RA | 726,800 | A→G | A79A (GCT→GCC) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 764,359 | C→T | A60A (GCC→GCT) | sucD → | succinyl‑CoA synthetase subunit alpha |
| RA | 775,359 | C→T | S69S (AGC→AGT) | tolQ → | Tol‑Pal system protein TolQ |
| RA | 796,360 | A→G | T167A (ACC→GCC) | modB → | molybdate ABC transporter membrane subunit |
| RA | 842,009 | (GA)4→3 | coding (47‑48/261 nt) | mcbA ← | DUF1471 domain‑containing protein McbA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 893,579 | T→C | intergenic (+146/‑205) | ybjN → / → potF | protein YbjN/putrescine ABC transporter periplasmic binding protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 936,549 | T→C | V1109A (GTG→GCG) | ftsK → | cell division DNA translocase FtsK |
| RA | 995,625 | A→G | F122L (TTC→CTC) | ssuD ← | FMNH2‑dependent alkanesulfonate monooxygenase |
| RA | 1,002,950 | T→C | V21A (GTC→GCC) | ycbU → | putative fimbrial protein YcbU |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,074,398 | A→G | T53A (ACC→GCC) | rutR → | DNA‑binding transcriptional dual regulator RutR |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,163,379 | A→G | E40E (GAA→GAG) | thiK → | thiamine kinase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,316,315 | T→C | intergenic (‑280/+101) | yciG ← / ← trpA | protein YciG/tryptophan synthase subunit alpha |
| RA | 1,329,979 | C→T | S216S (AGC→AGT) | sohB → | S49 peptidase family protein |
| RA | 1,377,805 | A→G | D325G (GAC→GGC) | ycjS → | putative oxidoreductase YcjS |
| RA | 1,515,631 | A→G | K18K (AAA→AAG) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,750,415 | A→G | L200P (CTA→CCA) | ydhX ← | putative 4Fe‑4S ferredoxin‑type protein |
| RA | 1,810,873 | T→C | intergenic (+72/‑61) | ydjM → / → tcyP | putative inner membrane protein regulated by LexA/cystine/sulfocysteine:cation symporter |
| RA | 1,815,787 | A→G | T641A (ACT→GCT) | katE → | catalase II |
| RA | 1,834,213 | C→T | A33V (GCG→GTG) | ydjY → | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY |
| RA | 1,844,405 | T→C | D156G (GAC→GGC) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,904,017 | T→C | G41G (GGT→GGC) | manZ → | mannose‑specific PTS enzyme IID component |
| RA | 1,906,993 | T→C | Q23R (CAG→CGG) | rlmA ← | 23S rRNA m(1)G745 methyltransferase |
| RA | 1,930,522 | T→C | K76E (AAA→GAA) | yebG ← | DNA damage‑inducible protein YebG |
| RA | 1,933,861 | A→G | H248H (CAT→CAC) | edd ← | phosphogluconate dehydratase |
| RA | 1,948,292 | A→G | V114A (GTT→GCT) | nudB ← | dihydroneopterin triphosphate diphosphatase |
| RA | 1,954,688 | A→G | S774P (TCG→CCG) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,002,309 | T→C | N433S (AAC→AGC) | fliC ← | flagellar filament structural protein |
| RA | 2,030,309 | T→C | G257G (GGT→GGC) | yedA → | putative transporter YedA |
| RA | 2,107,972 | (T)8→7 | coding (358/1104 nt) | glf ← | UDP‑galactopyranose mutase |
| RA | 2,125,561 | (C)5→6 | coding (186/1224 nt) | wcaI ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,137,847 | T→C | intergenic (‑604/‑55) | wza ← / → yegH | outer membrane polysaccharide export protein Wza/inner membrane protein YegH |
| RA | 2,169,070 | A→G | D120G (GAC→GGC) | yegS → | lipid kinase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,218,942 | T→C | K180K (AAA→AAG) | osmF ← | glycine betaine ABC transporter periplasmic binding protein OsmF |
| RA | 2,255,555 | (C)5→4 | coding (201/660 nt) | yeiL → | putative DNA‑binding transcriptional regulator YeiL |
| RA | 2,273,700 | T→C | V446A (GTA→GCA) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,278,610 | A→G | I384T (ATT→ACT) | bcr ← | multidrug efflux pump Bcr |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,328,560 | G→A | T413I (ACA→ATA) | yfaQ ← | tandem DUF2300 domain‑containing protein YfaQ |
| RA | 2,430,582 | C→T | R61Q (CGA→CAA) | cvpA ← | colicin V production protein |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,536,308 | G→A | V159M (GTG→ATG) | crr → | Enzyme IIA(Glc) |
| RA | 2,546,031 | A→G | T87A (ACC→GCC) | murQ → | N‑acetylmuramic acid 6‑phosphate etherase |
| RA | 2,590,960 | A→G | intergenic (‑94/‑287) | ypfM ← / → yffB | uncharacterized protein YpfM/putative reductase YffB |
| RA | 2,634,681 | T→C | G150G (GGT→GGC) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,767,507 | (C)7→8 | intergenic (+152/‑203) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,843,525 | C→T | W229* (TGG→TAG) | hycG ← | formate hydrogenlyase subunit HycG |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,863,847 | G→A | A85A (GCG→GCA) | ygbL → | putative 3‑oxo‑tetronate 4‑phosphate decarboxylase YgbL |
| RA | 2,878,312 | C→T | intergenic (+694/+257) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,921,571 | A→G | V177A (GTG→GCG) | gudP ← | galactarate/glucarate/glycerate transporter GudP |
| RA | 2,926,469 | G→A | L54L (TTG→TTA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,935,746 | T→C | C55R (TGT→CGT) | fucI → | L‑fucose isomerase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,962,357 | T→C | E24E (GAA→GAG) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,962,539 | T→C | T76A (ACA→GCA) | ppdC ← | putative YgdA |
| RA | 2,978,592 | A→G | V103A (GTT→GCT) | lysA ← | diaminopimelate decarboxylase |
| RA | 2,999,755 | (C)6→7 | coding (137/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,016,844 | A→G | Y262C (TAC→TGC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,077,404 | A→G | V18A (GTA→GCA) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,208,729 | T→C | F236L (TTC→CTC) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,226,612 | A→G | T127A (ACC→GCC) | ygjI → | putative transporter YgjI |
| RA | 3,234,091 | T→C | A18A (GCA→GCG) | higA ← | antitoxin/DNA‑binding transcriptional repressor HigA |
| RA | 3,236,458 | A→G | I167V (ATC→GTC) | ygjP → | putative metal‑dependent hydrolase |
| RA | 3,254,119 | T→C | G32G (GGA→GGG) | yhaJ ← | DNA‑binding transcriptional activator YhaJ |
| RA | 3,255,661 | C→T | G331R (GGG→AGG) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| 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 | 3,393,614 | G→A | A882V (GCC→GTC) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,468,483 | T→C | E457E (GAA→GAG) | chiA ← | endochitinase |
| RA | 3,488,756 | G→A | A656T (GCA→ACA) | yhfK → | putative transporter YhfK |
| RA | 3,490,764 | (C)5→4 | coding (66/564 nt) | pabA ← | aminodeoxychorismate synthase subunit 2 |
| RA | 3,543,556 | T→C | Y130Y (TAT→TAC) | rpnA → | recombination‑promoting nuclease RpnA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,650,680 | (C)7→6 | intergenic (+18/‑611) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,777,876 | T→C | C160R (TGC→CGC) | lldP → | lactate/glycolate:H(+) symporter LldP |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,856,300 | Δ1 bp | coding (8/348 nt) | yidH ← | conserved inner membrane protein YidH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,904,089 | C→T | L503L (TTG→TTA) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 4,135,283 | A→G | K483K (AAA→AAG) | katG → | hydroperoxidase I |
| RA | 4,200,155 | (C)6→7 | intergenic (+61/‑126) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,278,326 | (T)7→6 | intergenic (‑260/‑153) | ryjA ← / → ghxP | small RNA RyjA/guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,304,978 | A→G | G540G (GGT→GGC) | yjcS ← | alkyl sulfatase |
| RA | 4,334,450 | T→C | T381A (ACC→GCC) | eptA ← | phosphoethanolamine transferase EptA |
| RA | 4,361,490 | A→G | S149P (TCC→CCC) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,372,011 | C→T | T329T (ACC→ACT) | groL → | chaperonin GroEL |
| RA | 4,423,417 | C→T | A191V (GCG→GTG) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,470,361 | A→G | intergenic (+40/+166) | mgtA → / ← ridA | Mg(2(+)) importing P‑type ATPase/enamine/imine deaminase, redox regulated chaperone |
| RA | 4,551,796 | A→G | D54G (GAC→GGC) | uxuA → | D‑mannonate dehydratase |
| RA | 4,559,111 | A→G | V139A (GTC→GCC) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,563,468 | C→A | A46S (GCC→TCC) | yjiK ← | uncharacterized protein YjiK |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,619,525 | A→G | T433A (ACT→GCT) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1996850 | 1996976 | 127 | 27 [26] | [26] 27 | [sdsN] | [sdsN] |
| * | * | ÷ | NC_000913 | 2249596 | 2249714 | 119 | 27 [26] | [24] 27 | [yeiE] | [yeiE] |
| * | * | ÷ | NC_000913 | 3423766–3424233 | 3424531–3424238 | 6–766 | 28 [26] | [25] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3751907 | 3751986 | 80 | 27 [26] | [22] 31 | yiaT/yiaU | outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 89 (1.000) | 30 (0.380) | 25/246 | 1.8 | 32.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 46 (0.580) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (0.800) | 50/270 | 0.4 | 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 = | 129 (1.450) | 134 (1.520) | 64/276 | 0.1 | 67.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 121 (1.360) | 68/278 | 0.1 | 98.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||