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 | freq | annotation | gene | description |
| RA | 70,356 | C→A | 6.9% | G218V (GGG→GTG) ‡ | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,357 | C→T | 6.9% | G218R (GGG→AGG) ‡ | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,363 | Δ1 bp | 6.1% | coding (646/1611 nt) | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,364 | Δ1 bp | 6.1% | coding (645/1611 nt) | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,365 | A→G | 6.0% | L215P (CTA→CCA) | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,368 | Δ1 bp | 5.5% | coding (641/1611 nt) | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 70,370 | Δ1 bp | 5.8% | coding (639/1611 nt) | thiP ← | thiamine, thiamine pyrophosphate ABC transporter permease; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 88,592 | C→A | 13.6% | N231K (AAC→AAA) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3) |
| RA | 93,307 | A→G | 5.2% | L273L (TTA→TTG) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide transferase |
| RA | 95,552 | G→A | 5.1% | Q221Q (CAG→CAA) | ftsW → | lipid II flippase; integral membrane protein involved in stabilizing FstZ ring during cell division |
| RA | 141,748 | G→A | 6.8% | A61T (GCA→ACA) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 159,229 | G→T | 6.8% | G213V (GGA→GTA) | hrpB → | putative ATP‑dependent helicase |
| RA | 179,823 | C→A | 5.6% | P292T (CCT→ACT) | cdaR → | carbohydrate diacid regulon transcriptional regulator; autoregulator |
| RA | 180,552 | T→C | 5.4% | T11A (ACC→GCC) | yaeH ← | UPF0325 family protein |
| RA | 195,817 | A→G | 5.5% | Y468C (TAT→TGT) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| RA | 221,407 | A→T | 5.2% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 5.2% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 5.4% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 8.3% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 8.6% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 249,908 | A→G | 11.5% | intergenic (+260/‑58) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 260,759 | C→A | 5.6% | W53C (TGG→TGT) | yafX ← | CP4‑6 prophage; uncharacterized protein |
| RA | 277,094 | G→A | 5.1% | P201S (CCG→TCG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 286,409 | T→A | 7.7% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 337,136 | G→T | 6.4% | A101S (GCC→TCC) | yahJ → | putative metallo‑dependent hydrolase domain deaminase |
| RA | 372,887:1 | +A | 6.1% | intergenic (+120/+104) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,888 | C→G | 6.1% | intergenic (+121/+103) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 420,091 | T→C | 5.5% | D95G (GAC→GGC) | acpH ← | acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase |
| RA | 431,417 | C→T | 6.9% | L110F (CTT→TTT) | thiL → | thiamine monophosphate kinase |
| RA | 478,824 | C→A | 6.0% | E346* (GAA→TAA) | acrB ← | multidrug efflux system protein |
| RA | 520,562 | C→A | 6.5% | R616R (CGG→AGG) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 520,636 | G→A | 5.9% | E640E (GAG→GAA) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 520,654 | T→G | 5.3% | R646R (CGT→CGG) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 520,661 | A→C | 5.8% | S649R (AGC→CGC) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 573,883 | G→C | 5.3% | T107T (ACG→ACC) R34P (CGG→CCG) |
rzpD → rzoD → |
DLP12 prophage; putative murein endopeptidase DLP12 prophage; putative lipoprotein |
| RA | 592,104 | C→A | 5.5% | A350D (GCC→GAC) | cusC → | copper/silver efflux system, outer membrane component |
| RA | 627,941 | G→A | 7.8% | T331T (ACC→ACT) | ybdH ← | putative oxidoreductase |
| RA | 648,598 | G→T | 7.7% | R303L (CGG→CTG) | citA → | sensory histidine kinase in two‑component regulatory system with CitB |
| RA | 649,469 | C→T | 5.9% | P51L (CCG→CTG) | citB → | response regulator in two‑component regulatory system with CitA |
| RA | 654,377 | G→T | 5.7% | intergenic (+103/‑26) | ybeM → / → tatE | pseudogene, C‑N hydrolase superfamily homology;putative enzyme; Not classified; putative amidase/TatABCE protein translocation system subunit |
| RA | 701,992 | C→T | 5.1% | D148D (GAC→GAT) | glnS → | glutamyl‑tRNA synthetase |
| RA | 727,171 | T→G | 5.9% | N711K (AAT→AAG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,207 | C→T | 7.9% | R723R (CGC→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 8.6% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,560 | T→C | 7.5% | G1174G (GGT→GGC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 729,930 | A→G | 6.6% | pseudogene (342/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 783,126 | T→C | 6.6% | intergenic (‑75/+127) | gpmA ← / ← galM | phosphoglyceromutase 1/aldose 1‑epimerase; type‑1 mutarotase |
| RA | 897,023 | C→A | 7.1% | L228L (CTG→CTT) | artQ ← | arginine transporter subunit |
| RA | 908,193 | C→A | 6.3% | A360S (GCA→TCA) | hcp ← | hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases |
| RA | 946,992 | G→T | 5.5% | N673K (AAC→AAA) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 963,006 | C→T | 7.7% | R310R (CGC→CGT) | msbA → | fused lipid transporter subunits of ABC superfamily: membrane component/ATP‑binding component |
| RA | 998,746 | G→A | 8.0% | P134P (CCG→CCA) | ycbU → | putative fimbriae protein |
| RA | 1,029,072 | G→T | 6.6% | V121V (GTG→GTT) | hyaB → | hydrogenase 1, large subunit |
| RA | 1,056,237 | C→G | 8.2% | A509G (GCC→GGC) | torA → | trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit |
| RA | 1,105,460 | C→T | 6.9% | P224S (CCA→TCA) | opgG → | osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein |
| RA | 1,214,547 | C→A | 8.4% | L37M (CTG→ATG) | ymgF → | inner membrane division septum protein |
| RA | 1,259,313 | G→A | 6.1% | S48S (TCG→TCA) | hemA → | glutamyl tRNA reductase |
| RA | 1,259,400 | C→A | 14.4% | H77Q (CAC→CAA) | hemA → | glutamyl tRNA reductase |
| RA | 1,265,875 | T→C | 10.8% | noncoding (27/68 nt) | rdlC → | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC |
| RA | 1,282,249 | A→G | 15.9% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,599 | G→A | 10.6% | noncoding (94/171 nt) P12S (CCA→TCA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,608 | T→C | 11.4% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,617 | G→A | 10.7% | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,676 | A→G | 5.2% | noncoding (17/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| RA | 1,287,049 | T→C | 8.4% | V46A (GTG→GCG) | galU → | glucose‑1‑phosphate uridylyltransferase |
| RA | 1,368,394 | G→T | 5.8% | G16G (GGG→GGT) | ycjP → | inner membrane putative ABC superfamily sugar transporter permease |
| RA | 1,387,970 | G→T | 8.8% | A163S (GCC→TCC) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,408,527 | G→A | 9.7% | A175V (GCT→GTT) | recT ← | Rac prophage; recombination and repair protein |
| RA | 1,422,040 | A→G | 11.0% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,060 | G→C | 10.8% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,098 | G→A | 5.0% | pseudogene (886/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,219 | C→T | 5.7% | pseudogene (765/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,224 | T→G | 7.5% | pseudogene (760/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,228 | C→T | 7.4% | pseudogene (756/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 7.0% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,648 | G→C | 7.8% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,432,957 | G→A | 6.0% | C695C (TGC→TGT) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,457,738 | G→A | 8.3% | intergenic (+43/‑58) | paaK → / → paaX | phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,460,752 | C→T | 10.1% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 11.3% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,467,973 | C→A | 9.5% | pseudogene (3200/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,510,174 | G→T | 9.4% | A114S (GCG→TCG) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,522,209 | C→T | 5.7% | pseudogene (51/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,522,243 | C→T | 6.9% | pseudogene (85/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,523,601 | G→A | 10.3% | pseudogene (1443/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,526,984 | T→C | 5.9% | H304H (CAT→CAC) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,535,098 | G→A | 6.6% | R584C (CGC→TGC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,586,506 | T→A | 9.3% | E65V (GAA→GTA) | hipB ← | antitoxin of HipAB toxin‑antitoxin system |
| RA | 1,618,622 | C→A | 7.9% | D45Y (GAT→TAT) | ydeI ← | hydrogen peroxide resistance OB fold protein; putative periplasmic protein |
| RA | 1,629,727 | A→G | 5.3% | V126V (GTT→GTC) ‡ | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,629,728 | A→G | 5.3% | V126A (GTT→GCT) ‡ | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,629,823 | A→G | 6.4% | G94G (GGT→GGC) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,641,732 | C→A | 6.9% | pseudogene (162/279 nt) | ydfX ← | pseudogene, Qin prophage;Phage or Prophage Related |
| RA | 1,657,580 | G→A | 5.1% | G112S (GGC→AGC) | ynfG → | oxidoreductase, Fe‑S subunit |
| RA | 1,673,103 | C→A | 9.0% | I140I (ATC→ATA) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,702,935 | G→A | 9.8% | R587H (CGC→CAC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,966 | T→A | 12.1% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,725,778 | T→C | 10.5% | L812P (CTG→CCG) | lhr → | putative ATP‑dependent helicase |
| RA | 1,732,878 | G→T | 6.9% | E260* (GAA→TAA) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,752,177 | G→A | 8.3% | T269I (ACA→ATA) | ldtE ← | murein L,D‑transpeptidase |
| RA | 1,757,417 | C→T | 8.2% | V284I (GTA→ATA) | sufB ← | component of SufBCD Fe‑S cluster assembly scaffold |
| RA | 1,763,146 | C→A | 9.9% | intergenic (‑204/‑185) | ydiJ ← / → ydiK | putative FAD‑linked oxidoreductase/UPF0118 family inner membrane protein |
| RA | 1,789,064 | C→T | 5.3% | A116T (GCG→ACG) | btuC ← | vitamin B12 transporter subunit: membrane component of ABC superfamily |
| RA | 1,841,797 | C→T | 6.2% | V157I (GTA→ATA) | selD ← | selenophosphate synthase |
| RA | 1,869,403 | T→A | 6.2% | Q144L (CAG→CTG) | yeaM ← | putative DNA‑binding transcriptional regulator |
| RA | 1,931,572 | G→T | 12.1% | A222S (GCA→TCA) | yebK → | putative DNA‑binding transcriptional regulator |
| RA | 1,961,109 | G→A | 7.7% | T62T (ACC→ACT) | cheZ ← | chemotaxis regulator, protein phosphatase for CheY |
| RA | 2,009,308 | C→T | 5.8% | A316A (GCC→GCT) | fliG → | flagellar motor switching and energizing component |
| RA | 2,009,907 | C→A | 5.7% | R187S (CGC→AGC) | fliH → | negative regulator of FliI ATPase activity |
| RA | 2,013,547 | C→A | 6.2% | A150D (GCT→GAT) | fliL → | flagellar biosynthesis protein |
| RA | 2,019,914 | C→A | 6.4% | E529* (GAG→TAG) | yedQ ← | putative membrane‑anchored diguanylate cyclase |
| RA | 2,067,603 | G→T | 8.5% | A862S (GCC→TCC) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,133,928 | C→T | 7.0% | G389D (GGC→GAC) | asmA ← | suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,249,594 | A→G | 5.2% | T407T (ACT→ACC) | psuT ← | putative nucleoside transporter |
| RA | 2,249,608 | G→A | 5.3% | L403L (CTG→TTG) | psuT ← | putative nucleoside transporter |
| RA | 2,249,621 | T→C | 7.8% | A398A (GCA→GCG) | psuT ← | putative nucleoside transporter |
| RA | 2,249,624 | T→C | 7.8% | A397A (GCA→GCG) | psuT ← | putative nucleoside transporter |
| RA | 2,249,627 | T→C | 7.8% | A396A (GCA→GCG) | psuT ← | putative nucleoside transporter |
| RA | 2,257,691 | G→T | 6.1% | S117I (AGC→ATC) | setB → | lactose/glucose efflux system |
| RA | 2,272,928 | C→A | 8.1% | M104I (ATG→ATT) | bcr ← | bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,307,842 | G→A | 5.7% | L292L (CTG→CTA) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,370,570 | G→T | 5.4% | R168S (CGC→AGC) | menH ← | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| RA | 2,374,398 | C→T | 5.5% | V37I (GTT→ATT) | elaB ← | DUF883 family protein, putative membrane‑anchored ribosome‑binding protein |
| RA | 2,393,394 | G→T | 13.4% | A84E (GCG→GAG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,438,934 | C→A | 6.2% | G36W (GGG→TGG) | yfcA ← | UPF0721 family inner membrane protein |
| RA | 2,471,079 | C→T | 10.5% | R10R (CGG→CGA) | dsdC ← | dsd operon activator; autorepressor |
| RA | 2,516,832 | C→A | 7.6% | L171L (CTG→CTT) | xapB ← | xanthosine transporter |
| RA | 2,520,863 | G→T | 6.6% | D187Y (GAC→TAC) | yfeH → | putative inorganic ion transporter |
| RA | 2,530,059 | C→T | 9.3% | A180T (GCC→ACC) | pdxK ← | pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| RA | 2,534,658 | A→G | 6.7% | S127S (TCT→TCC) | cysW ← | sulfate/thiosulfate ABC transporter subunit |
| RA | 2,540,398 | C→A | 6.8% | P123T (CCG→ACG) | murP → | N‑acetylmuramic acid permease, EIIBC component, PTS system |
| RA | 2,564,645 | C→A | 7.4% | V156F (GTC→TTC) | eutE ← | aldehyde oxidoreductase, ethanolamine utilization protein |
| RA | 2,574,648 | A→G | 8.0% | I552V (ATT→GTT) | tktB → | transketolase 2, thiamine triphosphate‑binding |
| RA | 2,619,134 | A→T | 7.5% | K221* (AAA→TAA) | ppx → | exopolyphosphatase |
| RA | 2,630,508 | G→T | 5.3% | R70S (CGC→AGC) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,722,960 | T→A | 6.8% | intergenic (‑157/+15) | gltW ← / ← rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| RA | 2,757,696 | C→A | 7.8% | V273F (GTC→TTC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,762,984 | T→G | 9.9% | intergenic (+139/‑78) | yfjQ → / → yfjR | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,784,260 | G→T | 8.5% | R307L (CGC→CTC) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,790,576 | G→T | 6.1% | E3* (GAA→TAA) | ygaV → | tributyltin‑inducible repressor of ygaVP |
| RA | 2,805,658 | T→C | 5.5% | G291G (GGT→GGC) | emrA → | multidrug efflux system |
| RA | 2,805,659:1 | +C | 5.3% | coding (874/1173 nt) | emrA → | multidrug efflux system |
| RA | 2,805,659:2 | +G | 5.3% | coding (874/1173 nt) | emrA → | multidrug efflux system |
| RA | 2,805,659:3 | +C | 5.3% | coding (874/1173 nt) | emrA → | multidrug efflux system |
| RA | 2,805,659:4 | +A | 5.3% | coding (874/1173 nt) | emrA → | multidrug efflux system |
| RA | 2,805,660 | T→C | 5.3% | L292P (CTG→CCG) | emrA → | multidrug efflux system |
| RA | 2,805,663 | A→C | 7.3% | D293A (GAT→GCT) | emrA → | multidrug efflux system |
| RA | 2,805,664:1 | +G | 6.6% | coding (879/1173 nt) | emrA → | multidrug efflux system |
| RA | 2,805,666 | T→A | 6.6% | M294K (ATG→AAG) ‡ | emrA → | multidrug efflux system |
| RA | 2,805,667 | G→A | 6.3% | M294I (ATG→ATA) ‡ | emrA → | multidrug efflux system |
| RA | 2,809,704 | C→T | 6.4% | R32H (CGT→CAT) | gshA ← | glutamate‑cysteine ligase |
| RA | 2,811,683 | G→A | 5.7% | intergenic (‑50/+149) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,811,690 | G→T | 7.0% | intergenic (‑57/+142) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,842,897 | C→A | 6.1% | P104P (CCG→CCT) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,888,886 | A→G | 7.5% | C85R (TGC→CGC) | ygcQ ← | putative flavoprotein |
| RA | 2,904,833 | C→A | 5.4% | L726L (CTG→CTT) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,905,031 | G→T | 5.4% | S660R (AGC→AGA) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,940,824 | Δ1 bp | 7.0% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,940,826 | A→C | 7.0% | intergenic (+4/‑30) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,940,902 | G→A | 5.2% | noncoding (47/77 nt) | metW → | tRNA‑Met |
| RA | 2,981,545 | G→T | 5.9% | intergenic (+18/‑316) | yqeH → / → yqeI | putative LuxR family transcriptional regulator/putative transcriptional regulator |
| RA | 3,002,965 | C→T | 5.6% | A281A (GCC→GCT) | ygeY → | putative peptidase |
| RA | 3,030,035 | C→A | 9.3% | M477I (ATG→ATT) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,053,356 | G→A | 8.5% | G82D (GGC→GAC) | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,053,359 | Δ1 bp | 9.1% | coding (248/894 nt) | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,053,360 | T→C | 9.1% | D83D (GAT→GAC) | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,053,361 | G→A | 9.1% | E84K (GAA→AAA) ‡ | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,053,362 | A→T | 8.9% | E84V (GAA→GTA) ‡ | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,063,416 | T→G | 5.1% | intergenic (‑250/+108) | mscS ← / ← fbaA | mechanosensitive channel protein, small conductance/fructose‑bisphosphate aldolase, class II |
| RA | 3,064,664 | T→G | 5.1% | intergenic (‑61/+154) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,064,669 | G→A | 5.2% | intergenic (‑66/+149) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,133,045 | G→T | 5.8% | intergenic (+93/+30) | yghU → / ← hybG | putative S‑transferase/hydrogenase 2 accessory protein |
| RA | 3,149,035 | G→T | 5.7% | A108S (GCT→TCT) | yqhD → | aldehyde reductase, NADPH‑dependent |
| RA | 3,164,938 | C→T | 5.2% | R366C (CGC→TGC) | qseC → | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB |
| RA | 3,173,328 | G→A | 5.7% | E76K (GAA→AAA) | ygiB → | DUF1190 family protein |
| RA | 3,263,315 | T→C | 6.2% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,288,784 | C→A | 10.9% | P676T (CCC→ACC) P11H (CCC→CAC) |
lpoA → yraN → |
OM lipoprotein stimulator of MrcA transpeptidase UPF0102 family protein |
| RA | 3,295,709 | G→T | 6.0% | R289L (CGT→CTT) | yhbU → | U32 peptidase family protein |
| RA | 3,311,602 | T→C | 14.1% | noncoding (47/77 nt) | metY ← | tRNA‑Met |
| RA | 3,338,415 | G→T | 5.6% | G114C (GGC→TGC) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| RA | 3,345,913 | G→T | 6.4% | R158S (CGT→AGT) | arcB ← | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,350,795 | G→T | 6.7% | V904V (GTG→GTT) | gltB → | glutamate synthase, large subunit |
| RA | 3,385,539 | G→A | 5.9% | intergenic (‑152/+278) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,392,512 | C→A | 5.5% | G276C (GGC→TGC) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,416,899 | A→G | 5.8% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,470,686 | A→G | 5.1% | P31P (CCT→CCC) | fkpA ← | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 3,473,064 | C→T | 5.3% | L301L (CTG→CTA) | kefB ← | potassium:proton antiporter |
| RA | 3,473,917 | G→A | 5.9% | A17V (GCG→GTG) | kefB ← | potassium:proton antiporter |
| RA | 3,515,094 | C→A | 8.0% | E80* (GAA→TAA) | hofN ← | DNA catabolic putative fimbrial assembly protein |
| RA | 3,611,324 | G→A | 5.1% | S63S (TCG→TCA) | nikE → | nickel transporter subunit |
| RA | 3,614,441 | G→T | 5.3% | G630G (GGG→GGT) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,618,160 | A→G | 14.2% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,632,623 | G→T | 12.0% | intergenic (+122/+122) | pitA → / ← uspB | phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B |
| RA | 3,660,797 | A→G | 6.5% | D48D (GAT→GAC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,660,812 | A→G | 5.3% | F43F (TTT→TTC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,678,745 | C→A | 8.6% | P78P (CCG→CCT) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| RA | 3,822,340 | A→C | 11.9% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,833,019 | A→G | 5.6% | V112A (GTC→GCC) | nlpA ← | cytoplasmic membrane lipoprotein‑28 |
| RA | 3,949,697 | Δ1 bp | 7.4% | coding (1007/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,698 | Δ1 bp | 7.4% | coding (1008/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,699 | Δ1 bp | 7.4% | coding (1009/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,700 | Δ1 bp | 7.4% | coding (1010/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,701 | Δ1 bp | 7.4% | coding (1011/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,703 | Δ1 bp | 7.0% | coding (1013/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,704 | Δ1 bp | 7.0% | coding (1014/1545 nt) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,707 | G→T | 7.3% | A339A (GCG→GCT) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,712 | T→A | 7.4% | L341* (TTG→TAG) ‡ | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,949,713 | G→A | 7.7% | L341L (TTG→TTA) ‡ | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 3,976,013 | C→T | 7.5% | noncoding (48/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,996,977 | G→A | 5.6% | P188S (CCC→TCC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,000,259 | G→T | 8.5% | A346S (GCG→TCG) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,003,420 | G→T | 9.2% | P297P (CCG→CCT) | pldB → | lysophospholipase L2 |
| RA | 4,019,937 | C→T | 5.2% | T17T (ACC→ACT) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,042,364 | C→T | 6.3% | P680L (CCG→CTG) | polA → | fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease |
| RA | 4,063,817 | G→T | 10.1% | intergenic (‑56/+58) | yihR ← / ← yihS | mutarotase superfamily protein, YihR family/aldose‑ketose isomerase; D‑mannose isomerase |
| RA | 4,063,823 | T→A | 11.5% | intergenic (‑62/+52) | yihR ← / ← yihS | mutarotase superfamily protein, YihR family/aldose‑ketose isomerase; D‑mannose isomerase |
| RA | 4,063,824 | T→A | 11.6% | intergenic (‑63/+51) | yihR ← / ← yihS | mutarotase superfamily protein, YihR family/aldose‑ketose isomerase; D‑mannose isomerase |
| RA | 4,076,678 | A→G | 8.5% | R835R (CGT→CGC) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,076,681 | C→T | 8.7% | G834G (GGG→GGA) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,076,687 | G→C | 9.0% | G832G (GGC→GGG) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,076,694 | T→G | 9.9% | Q830P (CAG→CCG) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,087,233 | C→A | 7.3% | pseudogene (118/543 nt) | rhaD ← | pseudogene, truncated, rhamnulose‑phosphate aldolase |
| RA | 4,091,587 | G→T | 6.0% | intergenic (+229/‑31) | sodA → / → kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,143,298 | T→C | 6.3% | intergenic (‑272/+326) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,143,340 | T→C | 7.8% | intergenic (‑314/+284) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,149,083 | C→A | 8.0% | T222T (ACC→ACA) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,161,576 | A→C | 14.0% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,175,207 | G→T | 8.6% | intergenic (+6/‑71) | rpoB → / → rpoC | RNA polymerase, beta subunit/RNA polymerase, beta prime subunit |
| RA | 4,178,209 | C→T | 37.2% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 47.5% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,182,687 | G→T | 8.9% | Q27K (CAA→AAA) | thiS ← | immediate sulfur donor in thiazole formation |
| RA | 4,202,979 | A→C | 22.6% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,207,374 | C→T | 5.3% | P113L (CCG→CTG) | aceA → | isocitrate lyase |
| RA | 4,238,262 | G→T | 5.6% | G122C (GGC→TGC) | lamB → | maltose outer membrane porin (maltoporin) |
| RA | 4,285,988 | C→T | 11.0% | intergenic (+266/+265) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,304,378 | G→T | 5.5% | P181Q (CCG→CAG) | phnP ← | 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,315,705 | G→T | 6.1% | intergenic (‑147/+511) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,434,343 | G→A | 5.2% | A139T (GCA→ACA) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,447,037 | T→A | 7.4% | intergenic (+62/+94) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,039 | T→C | 6.1% | intergenic (+64/+92) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,041 | A→T | 6.2% | intergenic (+66/+90) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,045 | T→C | 6.1% | intergenic (+70/+86) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,047 | G→A | 6.1% | intergenic (+72/+84) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,063 | Δ1 bp | 6.2% | intergenic (+88/+68) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,066 | A→C | 6.1% | intergenic (+91/+65) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,447,067 | T→C | 6.1% | intergenic (+92/+64) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,463,327 | C→G | 6.2% | D182H (GAC→CAC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,478,341 | C→T | 5.5% | intergenic (+124/+37) | lptG → / ← yjgR | lipopolysaccharide export ABC permease of the LptBFGC export complex/DUF853 family protein with NTPase fold |
| RA | 4,499,743 | C→A | 9.3% | pseudogene (123/330 nt) | yjhV → | pseudogene, KpLE2 phage‑like element |
| RA | 4,508,444 | C→A | 9.1% | P34H (CCT→CAT) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,508,445 | T→C | 8.3% | P34P (CCT→CCC) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,508,690 | T→G | 5.7% | pseudogene (153/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,604,194 | C→T | 5.3% | intergenic (+117/+303) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 3448780 | 3448880 | 101 | 16 [15] | [15] 20 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3763078 | 3763264 | 187 | 16 [14] | [15] 20 | [yibV] | [yibV] |
| * | * | ÷ | CP009273 | 4249412 | 4249976 | 565 | 16 [15] | [15] 17 | zur | zur |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 335746 = | 61 (0.840) | 8 (0.110) | 5/246 | NT | 11.7% | noncoding (279/358 nt) | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | CP009273 | 372778 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 360104 = | 53 (0.730) | 50 (0.690) | 31/248 | NT | 48.5% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 370385 | 76 (1.450) | 22 (0.470) | 10/162 | NT | 24.3% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 627604 | NA (NA) | 3 (0.060) | 3/172 | NT | 8.9% | noncoding (34/34 nt) | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | CP009273 | 2284778 = | 31 (0.610) | noncoding (147/199 nt) | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | 1203246 = | 33 (0.460) | 23 (0.370) | 14/216 | NT | 41.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 36 (0.570) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 31 (0.430) | 17 (0.270) | 12/216 | NT | 35.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 36 (0.570) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1972777 | 43 (0.600) | 4 (0.060) | 3/248 | NT | 8.5% | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2283592 | NA (NA) | 105 (1.480) | 34/244 | NT | 89.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2399636 = | 12 (0.170) | coding (485/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes | |||||
| * | ? | CP009273 | = 2399639 | 12 (0.170) | 72 (1.000) | 32/248 | NT | 85.7% | coding (482/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes |
| ? | CP009273 | = 3124699 | NA (NA) | intergenic (+146/+1) | insH1/yghQ | IS5 transposase and trans‑activator/putative inner membrane polysaccharide flippase | |||||