mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 41,317 | A→G | G205G (GGT→GGC) | caiT ← | putative transporter |
| RA | 51,091 | A→G | G44G (GGT→GGC) | apaH ← | diadenosine tetraphosphatase |
| RA | 92,682 | A→G | T424A (ACA→GCA) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| RA | 186,439 | C→T | A738T (GCA→ACA) | glnD ← | uridylyltransferase |
| RA | 209,483 | C→T | A288V (GCG→GTG) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| JC JC | 238,963 | IS5 (+) +4 bp | pseudogene (137‑140/357 nt) | yafU ← | pseudogene |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 311,480 | (T)8→7 | intergenic (‑144/‑632) | ecpR ← / → ykgL | putative transcriptional regulator for the ecp operon/uncharacterized protein |
| RA | 328,638 | A→G | G32G (GGT→GGC) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 355,098 | T→C | G59G (GGT→GGC) | codB → | cytosine transporter |
| RA | 428,291 | C→T | S215S (AGC→AGT) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 479,603 | C→T | V106I (GTT→ATT) | maa ← | maltose O‑acetyltransferase |
| RA | 481,683 | (C)5→6 | coding (2721/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 551,656 | A→G | R313R (CGT→CGC) | purK ← | N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 627,982 | C→T | P97S (CCG→TCG) | entB → | isochorismatase |
| RA | 631,179 | A→G | N429S (AAC→AGC) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 635,382 | A→G | R396R (CGT→CGC) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 664,563 | A→G | S210P (TCT→CCT) | rlpA ← | septal ring protein, suppressor of prc, minor lipoprotein |
| RA | 666,076 | T→C | I80V (ATC→GTC) | mrdB ← | cell wall shape‑determining protein |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 750,703 | T→C | P489P (CCA→CCG) | ybgQ ← | putative outer membrane protein |
| RA | 788,591 | T→C | S83G (AGC→GGC) | galM ← | aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase |
| RA | 791,837 | A→G | A73A (GCT→GCC) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 852,223 | T→C | I125M (ATA→ATG) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 880,182 | T→C | D100G (GAC→GGC) | gstB ← | glutathione S‑transferase |
| RA | 942,837 | C→T | H627Y (CAT→TAT) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| JC JC | 944,912 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | intergenic (+16/+14) | dmsC → / ← ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase |
| RA | 949,117 | (T)5→4 | coding (452/909 nt) | ycaN ← | LysR family putative transcriptional regulator |
| RA | 999,721 | A→G | D169G (GAT→GGT) | elfC → | putative outer membrane fimbrial subunit export usher protein |
| RA | 1,011,526 | C→T | G521G (GGC→GGT) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,053,549 | A→G | L877P (CTA→CCA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,063,625 | C→T | E51K (GAA→AAA) | cbpA ← | DnaK co‑chaperone; curved DNA‑binding protein |
| RA | 1,066,324 | A→G | Q247R (CAG→CGG) | agp → | glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,077,452 | C→T | P477P (CCG→CCA) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,097,450 | T→C | intergenic (+621/+115) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,125,906 | G→A | W115* (TGG→TGA) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,148,553 | A→G | R311R (CGA→CGG) | plsX → | putative phosphate acyltransferase |
| RA | 1,262,619 | C→T | G87R (GGA→AGA) | ispE ← | 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
| RA | 1,386,502 | A→G | D331G (GAT→GGT) | ycjF → | UPF0283 family inner membrane protein |
| RA | 1,429,407 | T→C | V120A (GTG→GCG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,431,928 | T→C | S960S (AGT→AGC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,437,231 | (T)9→8 | intergenic (‑338/+29) | ompN ← / ← pfo | outer membrane pore protein N, non‑specific/pyruvate‑flavodoxin oxidoreductase |
| RA | 1,447,767 | T→C | R83R (CGT→CGC) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,452,630 | A→G | V338A (GTA→GCA) | paaZ ← | oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,460,132 | A→G | N360S (AAC→AGC) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| RA | 1,512,774 | A→G | Y374C (TAC→TGC) | ydcS → | putative ABC transporter periplasmic binding protein |
| RA | 1,525,931 | C→T | R17H (CGC→CAC) | ansP ← | L‑asparagine transporter |
| RA | 1,560,722 | A→G | Y70H (TAC→CAC) | ddpB ← | D,D‑dipeptide ABC transporter permease |
| RA | 1,681,679 | G→A | G235D (GGC→GAC) | folM → | dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme |
| RA | 1,735,191 | T→C | Y253H (TAC→CAC) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,745,624 | T→C | E168E (GAA→GAG) | ydhQ ← | autotransporter adhesin‑related protein |
| RA | 1,756,377 | T→C | L227P (CTC→CCC) | pykF → | pyruvate kinase I |
| RA | 1,764,710 | T→C | intergenic (‑324/+224) | sufA ← / ← ydiH | Fe‑S cluster assembly protein/uncharacterized protein |
| RA | 1,789,056 | T→C | F208L (TTC→CTC) | aroH → | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| RA | 1,815,591 | A→G | P575P (CCA→CCG) | katE → | catalase HPII, heme d‑containing |
| RA | 1,826,054 | T→C | E290E (GAA→GAG) | astE ← | succinylglutamate desuccinylase |
| RA | 1,881,694 | C→T | R39H (CGC→CAC) | dmlR ← | transcriptional activator of dmlA |
| RA | 1,882,431 | G→A | A174T (GCC→ACC) | dmlA → | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| RA | 1,897,602 | T→C | M224T (ATG→ACG) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,901,862 | T→C | intergenic (‑277/‑186) | yoaE ← / → manX | putative membrane protein/conserved protein/fused mannose‑specific PTS enzymes: IIA component/IIB component |
| RA | 1,937,537 | T→C | intergenic (+16/‑112) | yebK → / → pykA | putative DNA‑binding transcriptional regulator/pyruvate kinase II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,987,076 | T→C | V51A (GTG→GCG) | ftnB → | ferritin B, putative ferrous iron reservoir |
| RA | 1,989,945 | T→C | F89L (TTC→CTC) | tyrP → | tyrosine transporter |
| RA | 2,025,830 | T→C | L107P (CTA→CCA) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,064,506 | T→C | E239E (GAA→GAG) | cobS ← | cobalamin synthase |
| RA | 2,082,959 | T→C | G68G (GGT→GGC) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,098,022 | T→C | T94A (ACG→GCG) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,121,209 | A→G | Y116H (TAT→CAT) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,131,812 | G→A | R87C (CGC→TGC) | wcaC ← | putative glycosyl transferase |
| RA | 2,150,293 | A→G | D231D (GAT→GAC) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,165,605 | G→A | intergenic (+84/‑63) | yegP → / → yegQ | UPF0339 family protein/putative peptidase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,201,783 | T→C | V502A (GTA→GCA) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,262,101 | G→A | R89C (CGC→TGC) | fruK ← | fructose‑1‑phosphate kinase |
| RA | 2,262,375 | T→C | E374G (GAG→GGG) | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,274,782 | T→C | F202L (TTC→CTC) | yejB → | microcin C ABC transporter permease |
| RA | 2,328,783 | (G)5→6 | coding (1015/1650 nt) | yfaQ ← | tandem DUF2300 domain protein, putative host defense protein |
| RA | 2,337,019 | G→A | A801V (GCC→GTC) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,341,415 | T→C | T919A (ACG→GCG) | yfaL ← | adhesin |
| RA | 2,341,631 | T→C | T847A (ACT→GCT) | yfaL ← | adhesin |
| RA | 2,344,828 | T→C | intergenic (‑659/‑37) | yfaL ← / → nrdA | adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,353,790 | G→A | A382T (GCC→ACC) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,421,732 | A→G | T9A (ACA→GCA) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,482,332 | T→C | A336A (GCA→GCG) | emrK ← | multidrug resistance efflux pump membrane fusion protein |
| RA | 2,495,245 | G→A | S16S (AGC→AGT) | yfdY ← | DUF2545 family putative inner membrane protein |
| RA | 2,530,522 | T→C | S238G (AGC→GGC) | zipA ← | FtsZ stabilizer |
| RA | 2,548,346 | G→A | G82D (GGC→GAC) | yfeW → | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity |
| RA | 2,557,426 | T→C | L418L (TTA→TTG) | eutB ← | ethanolamine ammonia‑lyase, large subunit, heavy chain |
| RA | 2,660,902 | C→T | P210P (CCG→CCA) | iscS ← | cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent |
| RA | 2,674,912 | T→C | S284G (AGC→GGC) | yphC ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 2,695,244 | T→C | L100L (CTA→CTG) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,737,713 | (G)6→7 | intergenic (+67/‑32) | pheL → / → pheA | pheA gene leader peptide/chorismate mutase and prephenate dehydratase, P‑protein |
| RA | 2,776,212 | T→C | G98G (GGT→GGC) | yfjX → | CP4‑57 prophage; putative antirestriction protein |
| RA | 2,780,291 | G→A | G812G (GGC→GGT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,811,185 | T→C | L139P (CTC→CCC) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,815,388 | T→C | D351G (GAC→GGC) | gshA ← | glutamate‑cysteine ligase |
| RA | 2,830,245 | G→A | E145K (GAA→AAA) | srlQ → | D‑arabinose 5‑phosphate isomerase |
| RA | 2,924,303 | A→G | intergenic (‑190/+432) | yqcC ← / ← syd | DUF446 family protein/SecY‑interacting protein |
| RA | 2,955,355 | T→C | T217A (ACG→GCG) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 3,025,265 | T→C | G305G (GGT→GGC) | xanQ → | xanthine permease |
| RA | 3,057,204 | T→C | T403A (ACC→GCC) | serA ← | D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,065,588 | A→G | N263D (AAT→GAT) | scpC → | propionyl‑CoA:succinate CoA transferase |
| RA | 3,084,257 | T→C | Y552C (TAC→TGC) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,200,230 | C→T | G246S (GGC→AGC) | ygiF ← | inorganic triphosphatase |
| RA | 3,213,764 | C→T | R240C (CGC→TGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | sodium:serine/threonine symporter |
| RA | 3,267,728 | A→G | intergenic (+130/‑126) | tdcR → / → yhaB | L‑threonine dehydratase operon activator protein/uncharacterized protein |
| RA | 3,297,484 | G→A | R219C (CGC→TGC) | yraQ ← | putative inner membrane permease |
| RA | 3,377,215 | A→G | L69P (CTG→CCG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,542,564 | C→T | H720Y (CAT→TAT) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| RA | 3,560,455 | +G | 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 | 3,668,330 | G→A | P287S (CCG→TCG) | yhjA ← | putative cytochrome C peroxidase |
| RA | 3,750,344 | T→C | Y87H (TAT→CAT) | sgbE → | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 3,755,937 | A→G | V192A (GTG→GCG) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,842,330 | T→C | R25G (AGA→GGA) | yicN ← | DUF1198 family protein |
| RA | 3,925,463 | T→C | G57G (GGA→GGG) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,979,456 | G→A | D286N (GAC→AAC) | wzyE → | putative ECA polysaccharide chain elongation protein |
| RA | 4,079,433 | T→C | V46A (GTG→GCG) | yiiE → | CopG family putative transcriptional regulator |
| RA | 4,123,177 | T→C | T55A (ACG→GCG) | ftsN ← | essential cell division protein |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,145,072 | C→T | P360S (CCG→TCG) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,161,466 | G→A | G115S (GGC→AGC) | fabR → | transcriptional repressor of fabA and fabB |
| RA | 4,183,795 | A→G | T851A (ACC→GCC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,204,350 | A→G | Q344R (CAG→CGG) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,206,004 | G→A | A510V (GCC→GTC) | purH ← | IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,228,771 | A→G | E347E (GAA→GAG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,276,133 | A→G | K221K (AAA→AAG) | yjcC → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,339,912 | T→C | T204A (ACT→GCT) | adiA ← | arginine decarboxylase |
| RA | 4,352,500 | (A)8→7 | intergenic (+143/‑84) | yjdJ → / → ghoS | GNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,428,720 | T→C | intergenic (‑3/‑215) | ytfB ← / → fklB | OapA family protein/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 4,430,267 | A→G | D135G (GAC→GGC) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,454,344 | C→T | G254G (GGC→GGT) | yjfF → | putative sugar ABC transporter permease |
| RA | 4,492,667 | C→T | V229M (GTG→ATG) | idnO ← | 5‑keto‑D‑gluconate‑5‑reductase |
| RA | 4,500,381 | T→C | pseudogene (154/942 nt) | yjgX ← | pseudogene fragment |
| JC JC | 4,543,608 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| RA | 4,544,119 | T→C | V131A (GTA→GCA) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,560,233 | G→A | Q150* (CAG→TAG) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423726–3424234 | 3424588–3424238 | 5–863 | 40 [39] | [38] 40 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 18 (0.240) | 49 (0.720) | 43/266 | 1.1 | 74.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.270) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.240) | 70 (1.030) | 64/266 | 0.1 | 80.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.270) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 80 (1.080) | 69/290 | 0.1 | 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 | |||||