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 | 13,865 | C→T | A568V (GCG→GTG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 93,668 | A→G | E168G (GAG→GGG) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase |
| RA | 97,947 | T→C | R287R (CGT→CGC) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine:D‑glutamate ligase |
| RA | 146,238 | A→G | K386K (AAA→AAG) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 150,128 | A→G | S276P (TCT→CCT) | yadC ← | putative fimbrial‑like adhesin protein |
| RA | 170,771 | G→A | R66H (CGC→CAC) | fhuD → | iron(3+)‑hydroxamate import ABC transporter periplasmic binding protein |
| RA | 203,087 | T→C | G176G (GGT→GGC) | lpxA → | UDP‑N‑acetylglucosamine acetyltransferase |
| RA | 233,559 | T→C | T133A (ACG→GCG) | mltD ← | putative membrane‑bound lytic murein transglycosylase D |
| RA | 241,939 | A→G | C455C (TGT→TGC) | fadE ← | acyl coenzyme A dehydrogenase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 272,712 | (G)5→6 | intergenic (+523/‑135) | insN → / → ykfC | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/CP4‑6 prophage; conserved protein;Phage or Prophage Related |
| RA | 306,996 | G→A | N779N (AAC→AAT) | ecpC ← | ECP production outer membrane protein |
| RA | 308,755 | C→T | S193N (AGC→AAC) | ecpC ← | ECP production outer membrane protein |
| RA | 327,990 | T→C | E248E (GAA→GAG) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 349,825 | A→G | intergenic (+253/‑187) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 358,347 | G→A | A115V (GCG→GTG) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 359,143 | T→C | H115H (CAT→CAC) | cynT → | carbonic anhydrase |
| RA | 373,704 | G→A | V262M (GTG→ATG) | mhpF → | acetaldehyde‑CoA dehydrogenase II, NAD‑binding |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 396,691 | T→C | V18A (GTT→GCT) | sbmA → | peptide antibiotic transporter |
| RA | 396,736 | A→G | D33G (GAC→GGC) | sbmA → | peptide antibiotic transporter |
| RA | 398,614 | A→G | N248S (AAC→AGC) | yaiW → | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein |
| RA | 443,420 | A→G | G74G (GGT→GGC) | yajL ← | oxidative‑stress‑resistance chaperone |
| RA | 471,467 | A→G | T278A (ACC→GCC) | mdlB → | putative multidrug ABC transporter ATPase |
| RA | 483,728 | Δ1 bp | coding (676/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 485,845 | (G)5→6 | coding (85/648 nt) | acrR → | transcriptional repressor |
| RA | 514,375 | G→A | G128D (GGC→GAC) | cueR → | copper‑responsive regulon transcriptional regulator |
| RA | 516,951 | G→A | V123V (GTG→GTA) | fetB → | iron export ABC transporter permease; peroxide resistance protein |
| RA | 523,968 | C→T | G236G (GGC→GGT) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 549,698 | A→G | G24G (GGA→GGG) | ylbF → | putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein |
| RA | 563,150 | A→G | N272S (AAC→AGC) | sfmH → | FimA homolog, function unknown |
| RA | 573,991 | A→G | G12G (GGA→GGG) | quuD → | DLP12 prophage; putative antitermination protein |
| RA | 577,451 | T→C | G18G (GGT→GGC) | essD → | DLP12 prophage; putative phage lysis protein |
| RA | 592,635 | A→G | F182L (TTC→CTC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 597,758 | (G)5→6 | coding (280/1224 nt) | cusB → | copper/silver efflux system, membrane fusion protein |
| RA | 613,412 | C→T | P226S (CCC→TCC) | fes → | enterobactin/ferrienterobactin esterase |
| RA | 644,176 | C→T | intergenic (‑209/+21) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 646,110 | A→G | P157P (CCT→CCC) | citT ← | citrate/succinate antiporter; citrate carrier |
| RA | 684,342 | G→A | A24V (GCC→GTC) | rihA ← | ribonucleoside hydrolase 1 |
| RA | 686,137 | T→C | N178S (AAC→AGC) | gltJ ← | glutamate/aspartate ABC transporter permease |
| RA | 699,448 | A→G | intergenic (‑271/+126) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 699,862 | A→G | A155A (GCT→GCC) | umpH ← | UMP phosphatase |
| RA | 701,461 | (G)5→6 | coding (134/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 712,946 | C→T | intergenic (‑144/‑41) | ybfF ← / → seqA | acyl‑CoA esterase/negative modulator of initiation of replication |
| RA | 732,614 | A→G | D1011G (GAC→GGC) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| JC JC | 752,861 | IS5 (+) +4 bp | intergenic (‑66/+321) | ybgD ← / ← gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| RA | 768,591 | T→C | V205A (GTG→GCG) | mngB → | alpha‑mannosidase |
| RA | 780,929 | C→T | intergenic (+11/‑139) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 788,031 | T→C | K269K (AAA→AAG) | galM ← | aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase |
| RA | 798,688 | C→T | P35S (CCG→TCG) | pgl → | 6‑phosphogluconolactonase |
| RA | 811,250 | A→G | A290A (GCA→GCG) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 832,662 | T→C | M97V (ATG→GTG) | ybiA ← | DUF1768 family protein |
| RA | 846,072 | T→C | H131R (CAT→CGT) | glnQ ← | glutamine transporter subunit |
| RA | 902,979 | C→T | V4I (GTT→ATT) | artI ← | arginine transporter subunit |
| RA | 904,502 | T→C | intergenic (‑35/‑91) | ybjP ← / → ybjQ | lipoprotein/UPF0145 family protein |
| RA | 911,132 | A→G | intergenic (‑83/+50) | poxB ← / ← hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent |
| RA | 927,406 | A→G | H9H (CAT→CAC) | aat ← | leucyl/phenylalanyl‑tRNA‑protein transferase |
| RA | 944,703 | G→A | G224D (GGT→GAT) | dmsC → | dimethyl sulfoxide reductase, anaerobic, subunit C |
| RA | 973,216 | C→T | L62L (CTG→CTA) | elyC ← | envelope biogenesis factor; DUF218 superfamily protein |
| RA | 984,240 | A→G | T197T (ACA→ACG) | ycbL → | putative metal‑binding enzyme |
| RA | 1,010,983 | C→T | A340A (GCC→GCT) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,022,227 | A→G | Y553H (TAT→CAT) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| RA | 1,028,234 | A→G | T97A (ACT→GCT) | yccU → | putative CoA‑binding protein |
| RA | 1,042,663 | A→G | R516R (CGT→CGC) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,046,051 | A→G | V632A (GTA→GCA) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,072,718 | A→G | V49A (GTC→GCC) | rutB ← | ureidoacrylate amidohydrolase |
| RA | 1,103,122 | A→G | A25A (GCT→GCC) | csgD ← | csgBAC operon transcriptional regulator |
| RA | 1,119,351 | C→T | G33R (GGA→AGA) | yceO ← | uncharacterized protein |
| RA | 1,148,867 | A→G | T37A (ACC→GCC) | fabH → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,151,418 | A→G | intergenic (+14/‑197) | fabG → / → acpP | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase/acyl carrier protein (ACP) |
| RA | 1,174,596 | A→G | S190S (AGT→AGC) | ycfT ← | inner membrane protein |
| RA | 1,192,714 | A→G | C354R (TGC→CGC) | mnmA ← | tRNA(Gln,Lys,Glu) U34 2‑thiouridylase |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+615) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,213,552 | A→G | W170R (TGG→CGG) | bluR ← | repressor of blue light‑responsive genes |
| RA | 1,217,003 | A→G | intergenic (+7/‑325) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,225,048 | A→G | V105A (GTT→GCT) | minD ← | inhibitor of FtsZ ring polymerization; chromosome‑membrane tethering protein; membrane ATPase of the MinCDEE system |
| RA | 1,232,002 | C→T | R273W (CGG→TGG) | umuC → | translesion error‑prone DNA polymerase V subunit; DNA polymerase activity |
| RA | 1,243,818 | (T)5→4 | coding (710/735 nt) | ycgR ← | flagellar velocity braking protein, c‑di‑GMP‑regulated |
| RA | 1,260,849 | G→A | intergenic (‑46/+79) | dauA ← / ← prs | C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase |
| RA | 1,265,331 | A→G | D107G (GAC→GGC) | prfA → | peptide chain release factor RF‑1 |
| RA | 1,266,451 | A→G | T120A (ACC→GCC) | prmC → | RF‑1 and RF‑2 N5‑glutamine methyltransferase |
| RA | 1,302,933 | C→T | A12V (GCG→GTG) | oppB → | oligopeptide ABC transporter permease |
| RA | 1,313,733 | A→G | intergenic (‑70/‑287) | yciC ← / → ompW | UPF0259 family inner membrane protein/outer membrane protein W |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,369,520 | T→C | V43A (GTT→GCT) | pspD → | peripheral inner membrane phage‑shock protein |
| RA | 1,373,362 | T→C | N47N (AAT→AAC) | ycjO → | putative sugar ABC transporter permease |
| RA | 1,412,534 | T→C | E234E (GAA→GAG) | intR ← | Rac prophage; integrase |
| RA | 1,417,189 | A→G | A66A (GCT→GCC) | recE ← | Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,421,185 | T→C | Y23H (TAC→CAC) | ydaU → | Rac prophage; conserved protein |
| RA | 1,430,519 | T→C | S491P (TCA→CCA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,435,623 | A→G | intergenic (‑4/+137) | uspF ← / ← ompN | stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific |
| RA | 1,474,495 | A→G | D92G (GAC→GGC) | ydbC → | putative NAD(P)‑binding oxidoreductase |
| RA | 1,526,410 | C→T | T55I (ACA→ATA) | yncG → | glutathione S‑transferase homolog |
| RA | 1,527,726 | A→G | intergenic (+574/‑176) | yncH → / → rhsE | IPR020099 family protein/pseudogene, Rhs family |
| RA | 1,559,761 | T→C | S50S (TCA→TCG) | ddpC ← | D,D‑dipeptide ABC transporter permease |
| RA | 1,564,565 | A→G | L390P (CTG→CCG) | dosP ← | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| RA | 1,582,048 | A→G | G159G (GGT→GGC) | ydeN ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 1,583,067 | A→G | C207C (TGT→TGC) | ydeO ← | UV‑inducible global regulator, EvgA‑, GadE‑dependent |
| RA | 1,604,698 | A→G | T218A (ACG→GCG) | lsrD → | autoinducer 2 import system permease protein |
| RA | 1,608,413 | T→C | T204A (ACG→GCG) | yneE ← | bestrophin family putative inner membrane protein |
| RA | 1,618,274 | C→T | G212D (GGC→GAC) | marC ← | UPF0056 family inner membrane protein |
| RA | 1,618,445 | A→G | V155A (GTA→GCA) | marC ← | UPF0056 family inner membrane protein |
| RA | 1,621,321 | C→T | intergenic (‑184/‑11) | eamA ← / → ydeE | cysteine and O‑acetyl‑L‑serine efflux system/putative transporter |
| RA | 1,632,369 | T→C | intergenic (‑84/‑703) | ydfJ ← / → ydfK | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage |
| RA | 1,659,314 | A→G | T416A (ACC→GCC) | ynfE → | putative selenate reductase, periplasmic |
| RA | 1,663,917 | G→A | V103V (GTG→GTA) | ynfH → | oxidoreductase, membrane subunit |
| RA | 1,698,229 | T→C | M318V (ATG→GTG) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,711,501 | A→G | N225S (AAC→AGC) | rsxE → | SoxR iron‑sulfur cluster reduction factor component; electron transport inner membrane NADH‑quinone reductase |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme |
| RA | 1,751,240 | T→C | E162G (GAA→GGA) | ydhW ← | FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,773,044 | T→C | V178A (GTA→GCA) | ydiN → | putative MFS transporter, membrane protein |
| RA | 1,790,475 | T→C | Y257C (TAC→TGC) | ydiU ← | UPF0061 family protein |
| RA | 1,796,034 | A→G | R637R (CGT→CGC) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| RA | 1,802,726 | A→G | intergenic (‑156/‑368) | thrS ← / → arpB | threonyl‑tRNA synthetase/pseudogene, ankyrin repeats |
| RA | 1,803,324 | (T)5→4 | pseudogene (231/426 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,812,657 | (T)7→8 | coding (476/804 nt) | ydjO ← | uncharacterized protein |
| RA | 1,821,936 | A→T | D107E (GAT→GAA) | osmE ← | osmotically‑inducible lipoprotein |
| RA | 1,824,020 | T→C | L169P (CTG→CCG) | cho → | endonuclease of nucleotide excision repair |
| RA | 1,859,148 | A→G | F361S (TTC→TCC) | ydjK ← | putative MFS sugar transporter, membrane protein |
| RA | 1,865,882 | A→G | P197P (CCT→CCC) | mipA ← | scaffolding protein for murein synthesizing machinery |
| RA | 1,908,423 | C→T | Q42Q (CAG→CAA) | yebO ← | putative inner membrane protein |
| RA | 1,924,372 | T→C | T74A (ACA→GCA) | yebZ ← | inner membrane protein |
| RA | 1,938,397 | G→A | R250H (CGT→CAT) | pykA → | pyruvate kinase II |
| RA | 1,953,303 | T→C | M201T (ATG→ACG) | cmoA → | carboxy‑SAM synthase |
| RA | 1,967,611 | (C)5→6 | coding (891/1050 nt) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,009,257 | T→C | G327G (GGT→GGC) | yedE → | UPF0394 family sulphur transport domain‑containing inner membrane protein |
| RA | 2,010,754 | T→C | V52A (GTA→GCA) | yedL → | GNAT family putative N‑acetyltransferase |
| RA | 2,063,636 | T→C | M278V (ATG→GTG) | cobT ← | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,077,754 | G→A | A62A (GCG→GCA) | cbtA → | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| RA | 2,082,465 | G→A | S28L (TCA→TTA) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b |
| RA | 2,104,750 | T→C | H112R (CAC→CGC) | wbbJ ← | putative lipopolysaccharide biosynthesis O‑acetyl transferase |
| RA | 2,146,293 | C→T | R1010C (CGC→TGC) | yegE → | putative diguanylate cyclase |
| RA | 2,152,439 | C→T | G12R (GGA→AGA) | yegK ← | ser/thr phosphatase‑related protein |
| RA | 2,158,566 | T→C | S61P (TCT→CCT) | mdtC → | multidrug efflux system, subunit C |
| RA | 2,168,248 | A→G | V20A (GTG→GCG) | 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 | 2,182,120 | A→G | V221A (GTG→GCG) | yegW ← | putative DNA‑binding transcriptional regulator |
| RA | 2,182,939 | T→C | D238G (GAC→GGC) | yegX ← | putative family 25 glycosyl hydrolase |
| RA | 2,209,276 | G→A | pseudogene (177/2001 nt) | yehQ → | pseudogene |
| RA | 2,209,868 | A→G | pseudogene (769/2001 nt) | yehQ → | pseudogene |
| RA | 2,236,037 | G→A | G258D (GGT→GAT) | preA → | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C |
| RA | 2,243,790 | T→C | intergenic (‑138/‑120) | folE ← / → yeiG | GTP cyclohydrolase I/S‑formylglutathione hydrolase |
| RA | 2,246,914 | T→C | intergenic (‑145/+149) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,251,116 | G→A | D93N (GAT→AAT) | nfo → | endonuclease IV with intrinsic 3'‑5' exonuclease activity |
| RA | 2,265,230 | A→G | G22G (GGT→GGC) | yeiW ← | UPF0153 cysteine cluster protein |
| RA | 2,268,435 | G→A | A203T (GCC→ACC) | yeiR → | Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein |
| RA | 2,270,278 | T→C | R100R (CGT→CGC) | mepS → | murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase |
| RA | 2,287,209 | A→G | pseudogene (1706/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,304,235 | A→G | K111E (AAG→GAG) | eco → | ecotin, a serine protease inhibitor |
| RA | 2,311,405 | T→C | T44A (ACC→GCC) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| RA | 2,323,537 | A→G | T31A (ACT→GCT) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| RA | 2,355,663 | T→C | L48P (CTG→CCG) | glpC → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| RA | 2,360,846 | (C)5→6 | coding (569/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,398,634 | T→C | Q511R (CAG→CGG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,401,795 | G→A | R86R (CGC→CGT) | nuoE ← | NADH:ubiquinone oxidoreductase, chain E |
| RA | 2,437,826 | A→G | M9T (ATG→ACG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,445,152 | G→A | R137C (CGC→TGC) | yfcA ← | TauE/TSUP family inner membrane protein |
| RA | 2,459,668 | T→C | T268A (ACG→GCG) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| RA | 2,478,163 | T→C | V106A (GTG→GCG) | dsdX → | D‑serine transporter |
| RA | 2,488,952 | T→C | S73G (AGT→GGT) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,502,083 | A→G | R801R (CGT→CGC) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,502,713 | C→T | L591L (CTG→CTA) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,509,859 | G→A | S77N (AGC→AAC) | yfeO → | putative ion channel protein |
| RA | 2,516,313 | T→C | Y507C (TAC→TGC) | yfeA ← | putative diguanylate cyclase |
| RA | 2,527,658 | T→C | V238A (GTT→GCT) | yfeH → | putative inorganic ion transporter |
| RA | 2,567,770 | G→A | A113V (GCG→GTG) | eutH ← | ethanolamine transporter |
| RA | 2,576,775 | T→C | N535D (AAC→GAC) | maeB ← | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| RA | 2,578,155 | C→T | A75T (GCG→ACG) | maeB ← | malic enzyme: putative oxidoreductase/phosphotransacetylase |
| RA | 2,581,825 | T→C | Q318R (CAG→CGG) | ypfG ← | DUF1176 family protein |
| RA | 2,602,723 | G→A | R302R (CGG→CGA) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,678,816 | T→C | E184E (GAA→GAG) | yphF ← | putative sugar ABC transporter periplasmic binding protein |
| RA | 2,707,777 | C→T | V9I (GTC→ATC) | rseC ← | SoxR iron‑sulfur cluster reduction factor component |
| RA | 2,712,690 | A→G | C25C (TGT→TGC) | trmN ← | tRNA1(Val) (adenine(37)‑N6)‑methyltransferase |
| RA | 2,714,456 | T→C | S289G (AGT→GGT) | yfiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,740,735 | A→G | L139P (CTG→CCG) | aroF ← | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible |
| RA | 2,790,415 | T→C | V145A (GTC→GCC) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,795,142 | T→C | V297A (GTA→GCA) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,807,897 | A→G | T256A (ACC→GCC) | proX → | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein |
| RA | 2,811,185 | T→C | L139P (CTC→CCC) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,813,385 | A→G | N257S (AAC→AGC) | emrB → | multidrug efflux system protein |
| RA | 2,819,577 | A→G | V812A (GTT→GCT) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,837,983 | T→C | L41L (TTA→TTG) | hydN ← | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit |
| RA | 2,849,543 | G→A | R103C (CGT→TGT) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,862,791 | T→C | Y153H (TAT→CAT) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,862,827 | C→T | R165C (CGC→TGC) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,873,099 | 2 bp→CT | coding (238‑239/324 nt) | ygbE ← | DUF3561 family inner membrane protein |
| MC JC | 2,911,491 | Δ7,528 bp | [relA]–[gudD] | [relA], rlmD, barA, [gudD] | |
| RA | 2,923,308 | T→C | G159G (GGA→GGG) | truC ← | tRNA(Ile1,Asp) pseudouridine(65) synthase |
| RA | 2,937,090 | T→C | W503R (TGG→CGG) | fucI → | L‑fucose isomerase |
| RA | 2,942,711 | A→G | intergenic (‑144/+207) | gcvA ← / ← ygdI | glycine cleavage system transcriptional activator; autorepressor/DUF903 family verified lipoprotein |
| RA | 2,983,722 | T→C | T135A (ACG→GCG) | kduI ← | hexuronate isomerase |
| RA | 2,986,699 | T→C | L285L (TTG→CTG) | yqeG → | putative transporter |
| RA | 2,994,461 | (T)8→7 | pseudogene (632/633 nt) | ygeK ← | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator |
| RA | 3,000,899 | A→G | E185E (GAA→GAG) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,012,391 | T→C | *311Q (TAA→CAA) | yqeA → | putative amino acid kinase |
| RA | 3,016,166 | A→G | Y36C (TAC→TGC) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,019,115 | T→C | V1019A (GTC→GCC) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,039,247 | A→G | V166A (GTG→GCG) | xerD ← | site‑specific tyrosine recombinase |
| RA | 3,049,805 | (T)5→6 | coding (863/1095 nt) | gcvT ← | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex |
| RA | 3,083,334 | T→C | Y155C (TAT→TGT) | speB ← | agmatinase |
| RA | 3,108,362 | G→A | A265V (GCG→GTG) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,113,403 | A→G | C25C (TGT→TGC) | yghG ← | secretin (GspDbeta) OM localization lipoprotein pilotin |
| RA | 3,118,599 | C→T | V172I (GTT→ATT) | sslE ← | putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,130,088 | T→G | pseudogene (56/1101 nt) | yghO ← | pseudogene, IS‑interrupted |
| RA | 3,243,428 | T→C | E438E (GAA→GAG) | uxaC ← | uronate isomerase |
| RA | 3,244,516 | T→C | T76A (ACC→GCC) | uxaC ← | uronate isomerase |
| RA | 3,246,757 | C→T | R36C (CGC→TGC) | exuR → | hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,257,613 | G→A | A133V (GCC→GTC) | yhaO ← | putative transporter |
| RA | 3,286,334 | T→C | L22P (CTT→CCT) | agaI → | galactosamine‑6‑phosphate isomerase |
| RA | 3,288,276 | A→G | N63D (AAT→GAT) | yraI → | putative periplasmic pilin chaperone |
| RA | 3,296,292 | C→T | R162C (CGC→TGC) | diaA → | DnaA initiator‑associating factor for replication initiation |
| RA | 3,311,736 | G→A | intergenic (‑52/+97) | rpsO ← / ← truB | 30S ribosomal subunit protein S15/tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase |
| RA | 3,359,379 | T→C | V61A (GTA→GCA) | gltD → | glutamate synthase, 4Fe‑4S protein, small subunit |
| RA | 3,363,151 | T→C | G115G (GGT→GGC) | yhcD → | putative outer membrane fimbrial subunit usher protein |
| RA | 3,369,969 | T→A | T128S (ACC→TCC) | nanK ← | N‑acetylmannosamine kinase |
| RA | 3,376,341 | +G | coding (436/498 nt) | sspB ← | ClpXP protease specificity enhancing factor |
| RA | 3,379,933 | T→C | D22G (GAC→GGC) | zapE ← | divisome ATPase |
| RA | 3,416,884 | G→A | G618S (GGC→AGC) | acrF → | multidrug efflux system protein |
| RA | 3,434,764 | T→C | L184S (TTG→TCG) | fmt → | 10‑formyltetrahydrofolate:L‑methionyl‑tRNA(fMet) N‑formyltransferase |
| RA | 3,508,245 | T→C | T116A (ACG→GCG) | php ← | phosphotriesterase homology protein |
| RA | 3,514,996 | T→C | T22A (ACC→GCC) | rpe ← | D‑ribulose‑5‑phosphate 3‑epimerase |
| RA | 3,538,396 | A→G | T338A (ACT→GCT) | yhgF → | putative transcriptional accessory protein |
| RA | 3,539,032 | T→C | C550R (TGC→CGC) | yhgF → | putative transcriptional accessory protein |
| RA | 3,547,938 | T→C | intergenic (+63/+48) | gntT → / ← malQ | gluconate transporter, high‑affinity GNT I system/4‑alpha‑glucanotransferase (amylomaltase) |
| RA | 3,554,511 | T→C | L476P (CTG→CCG) | malT → | mal regulon transcriptional activator |
| RA | 3,555,945 | A→G | V302A (GTC→GCC) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| 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 | 3,636,796 | C→A | Q205H (CAG→CAT) | yhiN ← | putative oxidoreductase |
| RA | 3,687,764 | T→C | A470A (GCA→GCG) | bcsC ← | cellulose synthase subunit |
| RA | 3,693,594 | A→G | L548P (CTG→CCG) | bcsA ← | cellulose synthase, catalytic subunit |
| RA | 3,699,320 | T→C | A369A (GCT→GCC) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| RA | 3,733,738 | T→C | V513A (GTC→GCC) | xylG → | D‑xylose ABC transporter dual domain ATPase |
| RA | 3,785,668 | C→T | L137L (CTG→TTG) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
| RA | 3,844,363 | T→C | F134L (TTT→CTT) | adeD → | cryptic adenine deaminase |
| RA | 3,873,439 | G→A | D58D (GAC→GAT) | dgoA ← | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase |
| RA | 3,883,255 | C→T | D159N (GAT→AAT) | dnaA ← | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator |
| RA | 3,887,033 | G→A | G69D (GGC→GAC) | mnmE → | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase |
| RA | 3,906,128 | A→G | V147A (GTG→GCG) | bglG ← | transcriptional antiterminator of the bgl operon |
| RA | 3,913,871 | T→C | T444A (ACT→GCT) | glmU ← | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase |
| RA | 3,922,656 | T→C | intergenic (‑216/+401) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| RA | 3,925,611 | T→C | D8G (GAC→GGC) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,930,513 | T→C | Q194R (CAG→CGG) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,966,830 | G→A | P138P (CCG→CCA) | rho → | transcription termination factor |
| RA | 3,967,246 | T→C | V277A (GTT→GCT) | rho → | transcription termination factor |
| RA | 3,967,714 | C→T | intergenic (+38/‑202) | rho → / → wecA | transcription termination factor/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| RA | 3,969,685 | A→G | I219V (ATC→GTC) | wzzE → | Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein |
| RA | 3,970,062 | C→T | R344R (CGC→CGT) | wzzE → | Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein |
| RA | 3,991,678 | T→C | S176P (TCC→CCC) | cyaA → | adenylate cyclase |
| RA | 3,998,071 | G→T | G30V (GGC→GTC) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,009,349 | C→T | C60C (TGC→TGT) | pldB → | lysophospholipase L2 |
| RA | 4,009,947 | A→G | T260A (ACG→GCG) | pldB → | lysophospholipase L2 |
| RA | 4,082,219 | T→C | T181A (ACG→GCG) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,172,943 | A→G | D296G (GAC→GGC) | murB → | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| RA | 4,182,890 | A→G | D549G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,036 | T→C | V931A (GTT→GCT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,203,428 | A→G | S37G (AGC→GGC) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,221,741 | C→T | R249R (CGG→CGA) | arpA ← | ankyrin repeat protein |
| RA | 4,234,063 | T→C | R102R (CGT→CGC) | pgi → | glucosephosphate isomerase |
| RA | 4,265,952 | A→G | V57V (GTA→GTG) | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,286,249 | T→C | T375A (ACC→GCC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,317,201 | A→G | V6V (GTT→GTC) | phnM ← | ribophosphonate triphosphate hydrolase |
| RA | 4,319,158 | T→C | Y150C (TAC→TGC) | phnJ ← | carbon‑phosphorus lyase, SAM‑dependent |
| RA | 4,347,323 | A→G | S2P (TCA→CCA) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,351,153 | G→A | S170S (AGC→AGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,358,354 | A→G | T88T (ACT→ACC) | cadA ← | lysine decarboxylase, acid‑inducible |
| MC JC | 4,398,054 | Δ7 bp | coding (643‑649/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,403,176 | C→T | P380L (CCG→CTG) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 4,445,200 | G→A | W363* (TGG→TGA) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,457,566 | C→T | A100A (GCG→GCA) | yjgA ← | ribosome‑associated UPF0307 family protein |
| RA | 4,485,806 | Δ1 bp | coding (146/1512 nt) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,511,130 | G→A | R110C (CGT→TGT) | fecE ← | ferric citrate ABC transporter ATPase |
| RA | 4,513,844 | T→C | A155A (GCA→GCG) | fecB ← | ferric citrate ABC transporter periplasmic binding protein |
| RA | 4,517,263 | T→C | Y152C (TAC→TGC) | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,535,254 | A→G | pseudogene (252/1029 nt) | yjhR → | pseudogene, helicase family; putative frameshift suppressor |
| 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 | 4,550,166 | A→G | T377T (ACT→ACC) | gntP ← | fructuronate transporter |
| RA | 4,556,769 | (T)9→10 | intergenic (‑449/‑224) | yjiC ← / → iraD | uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,577,694 | G→A | H89Y (CAT→TAT) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC |
| RA | 4,586,594 | (G)6→5 | coding (168/3513 nt) | hsdR ← | endonuclease R Type I restriction enzyme |
| RA | 4,608,413 | C→T | R77C (CGT→TGT) | rimI → | ribosomal‑protein‑S18‑alanine N‑acetyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423731–3424234 | 3424578–3424238 | 5–848 | 26 [25] | [25] 26 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 8 (0.140) | 38 (0.740) | 36/266 | 0.7 | 83.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 8 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.140) | 43 (0.830) | 39/266 | 0.5 | 85.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 8 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 58 (1.030) | 48/290 | 0.3 | 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 | |||||