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 | 17,237 | A→G | intergenic (‑277/‑252) | mokC ← / → nhaA | regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter |
| RA | 24,819 | A→G | D810G (GAC→GGC) | ileS → | isoleucyl‑tRNA synthetase |
| RA | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl‑phosphate synthase large subunit/cai operon transcriptional activator |
| RA | 39,079 | C→T | A13T (GCC→ACC) | caiB ← | crotonobetainyl CoA:carnitine CoA transferase |
| RA | 51,996 | C→T | V145V (GTG→GTA) | rsmA ← | 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM‑dependent |
| RA | 124,759 | A→G | A581A (GCA→GCG) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 130,055 | G→A | S402S (AGC→AGT) | yacH ← | DUF3300 family protein |
| RA | 158,212 | A→G | R305R (CGT→CGC) | pcnB ← | poly(A) polymerase |
| RA | 158,903 | C→T | G75D (GGC→GAC) | pcnB ← | poly(A) polymerase |
| RA | 216,672 | A→G | V111A (GTC→GCC) | yaeF ← | putative lipoprotein |
| RA | 231,852 | T→C | V244A (GTA→GCA) | yafD → | endo/exonuclease/phosphatase family protein |
| RA | 250,026 | A→G | pseudogene (45/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 268,643 | C→T | A106A (GCG→GCA) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 276,808 | T→C | C32R (TGT→CGT) | mmuM → | CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase |
| RA | 282,361 | C→T | G28G (GGC→GGT) | yagE → | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| RA | 304,787 | G→A | P140L (CCG→CTG) | ecpE ← | ECP production pilus chaperone |
| RA | 368,846 | A→G | H79R (CAC→CGC) | mhpA → | 3‑(3‑hydroxyphenyl)propionate hydroxylase |
| RA | 372,097 | C→T | R287C (CGC→TGC) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 384,316 | C→G | A101P (GCC→CCC) | yaiS ← | putative PIG‑L family deacetylase |
| RA | 386,407 | A→G | G67G (GGA→GGG) | tauB → | taurine ABC transporter ATPase |
| RA | 393,298 | T→C | pseudogene (329/1449 nt) | yaiT → | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 411,433 | A→G | L350P (CTG→CCG) | araJ ← | L‑arabinose‑inducible putative transporter, MFS family |
| RA | 415,168 | C→T | A196T (GCC→ACC) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 447,954 | A→G | I31I (ATT→ATC) | cyoD ← | cytochrome o ubiquinol oxidase subunit IV |
| RA | 471,711 | A→G | N359S (AAC→AGC) | mdlB → | putative multidrug ABC transporter ATPase |
| RA | 562,582 | A→G | T83A (ACT→GCT) | sfmH → | FimA homolog, function unknown |
| RA | 571,192 | T→A | D100E (GAT→GAA) | ybcL → | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; UPF0098 family secreted protein |
| RA | 602,667 | G→A | D237N (GAT→AAT) | pheP → | phenylalanine transporter |
| RA | 624,671 | A→G | intergenic (‑161/‑214) | fepB ← / → entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| RA | 648,555 | A→G | R339R (CGT→CGC) | citF ← | citrate lyase, citrate‑ACP transferase (alpha) subunit |
| RA | 649,250 | C→T | V108I (GTA→ATA) | citF ← | citrate lyase, citrate‑ACP transferase (alpha) subunit |
| RA | 649,679 | A→G | V271A (GTG→GCG) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 671,974 | G→A | D71D (GAC→GAT) | lptE ← | LPS assembly OM complex LptDE, lipoprotein component |
| RA | 785,340 | T→C | intergenic (‑23/‑293) | ybgS ← / → aroG | putative periplasmic protein/3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible |
| RA | 914,373 | A→G | V162A (GTC→GCC) | ybjE ← | putative transporter |
| RA | 935,434 | A→G | E737E (GAA→GAG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| 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 | 953,431 | A→G | S42P (TCC→CCC) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 1,022,355 | A→G | L510S (TTA→TCA) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| RA | 1,087,671 | T→C | H59R (CAC→CGC) | pgaC ← | biofilm PGA synthase PgaCD, catalytic subunit; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase |
| RA | 1,091,158 | T→C | T378A (ACC→GCC) | pgaA ← | biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,109,893 | C→T | R187C (CGC→TGC) | opgG → | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| RA | 1,124,108 | (G)6→7 | intergenic (‑54/+10) | grxB ← / ← mdtH | glutaredoxin 2 (Grx2)/multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin |
| RA | 1,142,200 | C→T | R723H (CGT→CAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,192,212 | A→G | D140D (GAT→GAC) | hflD ← | putative lysogenization regulator |
| RA | 1,232,757 | T→C | T92A (ACC→GCC) | dsbB ← | oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| RA | 1,257,682 | A→G | V44A (GTA→GCA) | ychF ← | catalase inhibitor protein; ATPase, K+‑dependent, ribosome‑associated |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,307,511 | A→G | W379R (TGG→CGG) | clsA ← | cardiolipin synthase 1 |
| RA | 1,356,140 | T→C | N324S (AAC→AGC) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| JC JC | 1,393,457 | IS186 (–) +5 bp | coding (231‑235/1614 nt) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,400,721 | A→G | F351F (TTT→TTC) | abgT ← | p‑aminobenzoyl‑glutamate transporter; membrane protein |
| RA | 1,405,951 | C→T | intergenic (+302/‑28) | abgR → / → smrA | putative DNA‑binding transcriptional regulator of abgABT operon/DNA endonuclease |
| RA | 1,429,684 | A→G | S212S (TCA→TCG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,496,196 | A→G | R303R (CGA→CGG) | ydcJ → | putative metalloenzyme |
| RA | 1,568,898 | A→G | intergenic (‑75/+56) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,628,190 | A→G | H225R (CAC→CGC) | ydfG → | NADP‑dependent 3‑hydroxy acid dehydrogenase; malonic semialdehyde reductase |
| RA | 1,636,093 | G→A | pseudogene (275/528 nt) | nohQ ← | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| RA | 1,686,077 | A→G | L171P (CTG→CCG) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,696,856 | T→C | D66G (GAC→GGC) | uidR ← | transcriptional repressor |
| RA | 1,744,020 | C→T | L188L (CTC→CTT) | mdtK → | multidrug efflux system transporter |
| RA | 1,756,709 | G→A | V338M (GTG→ATG) | pykF → | pyruvate kinase I |
| RA | 1,768,945 | A→G | intergenic (‑260/‑129) | ydiJ ← / → ydiK | putative FAD‑linked oxidoreductase/UPF0118 family inner membrane protein |
| RA | 1,787,381 | A→G | intergenic (‑269/‑64) | ppsA ← / → ppsR | phosphoenolpyruvate synthase/PEP synthase kinase and PEP synthase pyrophosphorylase |
| RA | 1,811,829 | T→C | V299A (GTG→GCG) | ydjN → | putative transporter |
| RA | 1,840,491 | A→G | H342R (CAC→CGC) | ynjE → | molybdopterin synthase sulfurtransferase |
| RA | 1,843,898 | T→C | Y325C (TAC→TGC) | ynjI ← | inner membrane protein |
| RA | 1,856,991 | A→G | V260A (GTA→GCA) | ydjI ← | putative aldolase |
| RA | 1,931,374 | A→G | Q165R (CAG→CGG) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| RA | 1,938,582 | A→G | T312A (ACT→GCT) | pykA → | pyruvate kinase II |
| RA | 1,941,604 | G→A | A11V (GCG→GTG) | mepM ← | murein DD‑endopeptidase, space‑maker hydrolase, septation protein |
| RA | 1,951,184 | G→A | R118H (CGC→CAC) | yecD → | isochorismatase family protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,032,972 | C→T | T36T (ACG→ACA) | yedJ ← | putative HD superfamily phosphohydrolase |
| RA | 2,042,112 | T→C | intergenic (+87/‑256) | zinT → / → yodB | zinc and cadmium binding protein, periplasmic/cytochrome b561 homolog |
| RA | 2,130,545 | G→A | R112C (CGC→TGC) | wcaD ← | putative colanic acid polymerase |
| RA | 2,150,746 | T→C | G80G (GGA→GGG) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,168,019 | G→A | V96V (GTC→GTT) | yegR ← | uncharacterized protein |
| 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 | 2,178,383 | C→T | R61H (CGT→CAT) | fbaB ← | fructose‑bisphosphate aldolase class I |
| RA | 2,221,366 | T→C | K208K (AAA→AAG) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,224,823 | A→G | A16A (GCT→GCC) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,232,230 | T→C | C129C (TGT→TGC) | cdd → | cytidine/deoxycytidine deaminase |
| RA | 2,346,802 | G→A | A646A (GCG→GCA) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,366,486 | G→A | A187T (GCT→ACT) | arnB → | uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent |
| RA | 2,380,055 | T→C | T197A (ACT→GCT) | menF ← | isochorismate synthase 2 |
| RA | 2,386,502 | T→C | S215P (TCC→CCC) | yfbL → | putative M28A family peptidase |
| RA | 2,421,841 | T→C | V45A (GTG→GCG) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,427,402 | T→C | S130S (TCA→TCG) | argT ← | lysine/arginine/ornithine transporter subunit |
| RA | 2,438,860 | A→G | D304G (GAC→GGC) | flk → | putative flagella assembly protein |
| RA | 2,448,157 | T→C | N95S (AAC→AGC) | prmB ← | N5‑glutamine methyltransferase |
| RA | 2,474,212 | A→G | T61A (ACT→GCT) | yfdQ → | CPS‑53 (KpLE1) prophage; uncharacterized protein |
| RA | 2,475,549 | C→T | R13R (CGC→CGT) | yfdS → | CPS‑53 (KpLE1) prophage; uncharacterized protein |
| RA | 2,503,689 | A→G | I266T (ATT→ACT) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,559,936 | T→C | V360A (GTC→GCC) | intZ → | CPZ‑55 prophage; putative phage integrase |
| RA | 2,704,016 | A→G | T16T (ACT→ACC) | rnc ← | RNase III |
| RA | 2,715,479 | G→A | T19T (ACG→ACA) | eamB → | cysteine and O‑acetylserine exporter |
| RA | 2,720,149 | T→C | L66S (TTG→TCG) | pka → | protein lysine acetyltransferase |
| RA | 2,786,205 | T→C | intergenic (‑368/‑192) | ileY ← / → ygaQ | tRNA‑Ile/uncharacterized protein; putative enzyme |
| RA | 2,809,774 | (T)7→6 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,912,885 | A→G | I256T (ATC→ACC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,919,512 | G→A | A412V (GCC→GTC) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 3,041,565 | A→G | I85V (ATT→GTT) | ygfZ → | iron‑sulfur cluster repair protein, plumbagin resistance |
| RA | 3,061,828 | G→A | E327K (GAA→AAA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,062,799 | G→A | T650T (ACG→ACA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | DUF2884 family putative periplasmic protein |
| RA | 3,157,770 | A→G | T41A (ACT→GCT) | yqhG → | DUF3828 family putative periplasmic protein |
| RA | 3,280,131 | A→G | E406E (GAA→GAG) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,343,858 | T→C | V160A (GTA→GCA) | lptA → | lipopolysaccharide export ABC transporter periplasmic binding protein; Lipid A binding protein; LPS export and assembly protein |
| RA | 3,373,078 | T→C | T167A (ACC→GCC) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,376,927 | A→G | L165P (CTG→CCG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,386,861 | A→G | L443P (CTG→CCG) | aaeB ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,423,401 | A→G | intergenic (+207/+22) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,431,635 | G→A | R110W (CGG→TGG) | yrdD ← | ssDNA‑binding protein, function unknown |
| RA | 3,505,488 | A→G | V178A (GTG→GCG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family 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 | 3,575,211 | T→C | A47A (GCT→GCC) | yhgN → | UPF0056 family inner membrane protein |
| RA | 3,592,873 | T→C | T189A (ACT→GCT) | livF ← | branched‑chain amino acid ABC transporter ATPase |
| RA | 3,619,262 | C→T | A24V (GCC→GTC) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,622,455 | T→C | S1088S (AGT→AGC) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,623,539 | T→C | G47G (GGT→GGC) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 3,710,555 | A→G | intergenic (‑80/+244) | eptB ← / ← yhjX | KDO phosphoethanolamine transferase, Ca(2+)‑inducible/pyruvate‑inducible inner membrane protein, putative transporter |
| RA | 3,719,650 | T→C | V58A (GTA→GCA) | yiaG → | HTH_CROC1 family putative transcriptional regulator |
| RA | 3,811,334 | A→G | R28R (CGT→CGC) | rpmG ← | 50S ribosomal subunit protein L33 |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,816,407 | G→A | pseudogene (143/669 nt) | rph ← | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,819,035 | T→C | Y54Y (TAT→TAC) | yicG → | UPF0126 family inner membrane protein |
| RA | 3,855,661 | A→G | F104L (TTT→CTT) | yidG ← | inner membrane protein |
| RA | 3,856,193 | G→A | L39F (CTT→TTT) | yidH ← | DUF202 family inner membrane protein |
| RA | 3,899,764 | C→T | G272S (GGC→AGC) | yieL ← | putative xylanase |
| RA | 3,929,378 | A→G | C76R (TGC→CGC) | viaA ← | stimulator of RavA ATPase activity; von Willebrand factor domain protein |
| RA | 4,040,701 | A→G | intergenic (+65/+205) | rrfA → / ← mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,128,197 | T→C | T67A (ACC→GCC) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,150,087 | A→G | V60A (GTA→GCA) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,223,586 | C→T | V15I (GTT→ATT) | iclR ← | transcriptional repressor |
| RA | 4,254,807 | C→T | D554N (GAT→AAT) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,270,398 | A→G | N54S (AAC→AGC) | yjbQ → | thiamine phosphate synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,337,788 | A→G | S48P (TCC→CCC) | adiY ← | adi system transcriptional activator |
| RA | 4,390,985 | C→T | E175E (GAG→GAA) | rsgA ← | ribosome small subunit‑dependent GTPase A |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,408,885 | (A)6→5 | coding (2232/2442 nt) | rnr → | exoribonuclease R, RNase R |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,431,878 | T→C | T36A (ACG→GCG) | ytfE ← | iron‑sulfur cluster repair protein RIC |
| RA | 4,503,797 | A→G | intergenic (‑366/‑261) | insG ← / → yjhB | IS4 transposase/putative MFS transporter, membrane protein |
| RA | 4,550,829 | C→T | L156L (CTG→CTA) | gntP ← | fructuronate transporter |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423733–3424234 | 3424588–3424238 | 5–856 | 34 [32] | [33] 34 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3944126–3946158 | 3946158 | 1–2033 | 35 [32] | [33] 36 | rrlC | 23S ribosomal RNA of rrnC operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 11 (0.160) | 46 (0.760) | 40/266 | 0.9 | 82.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.170) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.160) | 44 (0.730) | 41/266 | 0.9 | 81.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.170) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||