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 | 1,502 | C→A | 11.8% | P389Q (CCG→CAG) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 51,492 | C→A | 6.7% | G39W (GGG→TGG) | apaG ← | protein associated with Co2+ and Mg2+ efflux |
| RA | 68,625 | C→A | 8.4% | intergenic (+23/+91) | yabI → / ← thiQ | DedA family inner membrane protein/thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 243,966 | C→T | 17.1% | intergenic (+18/‑158) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,983 | G→A | 10.8% | intergenic (+35/‑141) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,985 | A→G | 12.8% | intergenic (+37/‑139) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,991 | G→A | 10.2% | intergenic (+43/‑133) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 249,410 | C→A | 15.0% | S72Y (TCC→TAC) | yafP → | putative acyl‑CoA transferase |
| RA | 249,874 | G→C | 9.1% | intergenic (+226/‑92) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 258,669 | T→G | 10.9% | intergenic (+12/+192) | thrW → / ← ykfN | tRNA‑Thr/pseudogene, YdiA family |
| RA | 258,670 | T→A | 9.5% | intergenic (+13/+191) | thrW → / ← ykfN | tRNA‑Thr/pseudogene, YdiA family |
| RA | 262,071 | G→T | 6.9% | P65H (CCC→CAC) | yafY ← | lipoprotein, inner membrane; overproduction stimulates degP expression; CP4‑6 prophage |
| RA | 262,526 | C→T | 13.9% | pseudogene (153/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 262,529 | C→T | 13.6% | pseudogene (150/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 285,191 | G→A | 6.1% | P276S (CCG→TCG) | argF ← | ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 316,347 | C→A | 14.7% | A137E (GCA→GAA) | rclR → | reactive chlorine species (RCS)‑specific activator of the rcl genes |
| RA | 408,365 | G→T | 15.3% | R949S (CGT→AGT) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 495,179:2 | +T | 7.3% | coding (251/960 nt) | aes ← | acetyl esterase |
| RA | 495,179:4 | +C | 7.3% | coding (251/960 nt) | aes ← | acetyl esterase |
| RA | 495,179:5 | +A | 7.3% | coding (251/960 nt) | aes ← | acetyl esterase |
| RA | 571,358 | C→A | 10.8% | pseudogene (924/1040 nt) | nmpC ← | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 584,254 | C→A | 7.6% | L719L (CTG→CTT) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| RA | 599,005 | C→A | 10.9% | W372L (TGG→TTG) | ybdG ← | mechanosensitive channel protein, miniconductance |
| RA | 635,998 | Δ1 bp | 6.7% | coding (790/1566 nt) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 635,999 | Δ1 bp | 6.9% | coding (791/1566 nt) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 636,000 | Δ1 bp | 7.0% | coding (792/1566 nt) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 636,002 | Δ1 bp | 6.1% | coding (794/1566 nt) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 636,003 | Δ1 bp | 6.1% | coding (795/1566 nt) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 667,595 | G→T | 12.7% | T16T (ACC→ACA) | lptE ← | LPS assembly OM complex LptDE, lipoprotein component |
| RA | 700,576 | G→T | 9.3% | A393S (GCA→TCA) | nagE → | fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components |
| RA | 709,338 | G→T | 8.5% | V109F (GTC→TTC) | pgm → | phosphoglucomutase |
| RA | 714,378 | G→T | 6.6% | F513L (TTC→TTA) | speF ← | ornithine decarboxylase isozyme, inducible |
| RA | 726,406 | C→A | 6.2% | I456I (ATC→ATA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 8.4% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,330 | C→T | 5.1% | pseudogene (742/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 730,479 | C→G | 5.9% | pseudogene (891/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 740,827 | C→T | 7.4% | S69S (AGC→AGT) | ybgL → | UPF0271 family protein |
| RA | 773,475 | Δ1 bp | 5.5% | coding (280/1293 nt) | tolB → | periplasmic protein |
| RA | 773,476 | Δ1 bp | 5.5% | coding (281/1293 nt) | tolB → | periplasmic protein |
| RA | 773,481 | Δ1 bp | 5.1% | coding (286/1293 nt) | tolB → | periplasmic protein |
| RA | 773,482 | Δ1 bp | 5.1% | coding (287/1293 nt) | tolB → | periplasmic protein |
| RA | 773,483 | Δ1 bp | 5.1% | coding (288/1293 nt) | tolB → | periplasmic protein |
| RA | 773,487 | Δ1 bp | 5.1% | coding (292/1293 nt) | tolB → | periplasmic protein |
| RA | 786,024 | T→C | 7.8% | K154K (AAA→AAG) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 788,549 | C→A | 14.3% | A232A (GCG→GCT) | modF ← | fused molybdate transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 794,456 | C→T | 16.4% | R139C (CGT→TGT) | pgl → | 6‑phosphogluconolactonase |
| RA | 831,111 | G→A | 11.8% | T136T (ACG→ACA) | ybiB → | putative family 3 glycosyltransferase |
| RA | 833,742 | C→T | 10.8% | V57V (GTG→GTA) | ybiI ← | DksA‑type zinc finger protein |
| RA | 838,035 | G→T | 9.5% | R83L (CGG→CTG) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 841,463 | C→T | 7.0% | V153M (GTG→ATG) | glnQ ← | glutamine transporter subunit |
| RA | 848,419 | C→A | 11.2% | S12I (AGT→ATT) | mntS ← | Mn(2)‑response protein, MntR‑repressed |
| RA | 862,169 | C→T | 6.9% | A49V (GCG→GTG) | iaaA → | Isoaspartyl peptidase |
| RA | 880,707 | G→T | 10.2% | intergenic (‑21/+65) | ybjH ← / ← ybjI | uncharacterized protein/5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis |
| RA | 898,596 | G→T | 12.1% | H199N (CAC→AAC) | artP ← | arginine transporter subunit |
| RA | 903,647 | G→A | 13.3% | A31V (GCG→GTG) | ybjT ← | putative NAD‑dependent oxidoreductase |
| RA | 921,306 | A→G | 5.9% | intergenic (+310/+34) | clpA → / ← serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| RA | 941,814 | G→T | 5.5% | W163L (TGG→TTG) | ycaD → | putative MFS‑type transporter |
| RA | 1,003,206:1 | +A | 17.2% | intergenic (‑150/‑94) | ycbX ← / → rlmL | 6‑N‑hydroxylaminopurine detoxification oxidoreductase/fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent |
| RA | 1,016,418 | C→A | 100% | intergenic (‑43/‑176) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| RA | 1,045,283 | T→G | 10.1% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,100,068 | G→A | 13.8% | A56T (GCA→ACA) | csgA → | curlin subunit, amyloid curli fibers, cryptic |
| RA | 1,168,779 | C→T | 18.5% | A214A (GCG→GCA) | mfd ← | transcription‑repair coupling factor |
| RA | 1,199,962 | C→A | 6.1% | pseudogene (103/1134 nt) | aaaE → | pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related |
| RA | 1,209,043 | Δ1 bp | 7.5% | coding (473/732 nt) | bluR ← | repressor of blue light‑responsive genes |
| RA | 1,224,812 | G→A | 13.3% | intergenic (+80/+127) | ycgN → / ← hlyE | UPF0153 family cysteine cluster protein/hemolysin E |
| RA | 1,262,186 | G→T | 20.0% | G213* (GGA→TGA) | prmC → | N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2 |
| RA | 1,265,975 | C→T | 5.2% | intergenic (+59/+230) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,266,001 | G→T | 11.8% | intergenic (+85/+204) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,282,421 | A→G | 7.4% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,430 | C→T | 6.5% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,617 | G→A | 5.8% | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,323,037 | T→C | 11.8% | E111E (GAA→GAG) | yciK ← | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase |
| RA | 1,327,746 | G→T | 10.8% | L814L (CTG→CTT) | topA → | DNA topoisomerase I, omega subunit |
| RA | 1,331,484 | A→G | 8.1% | K466R (AAA→AGA) | acnA → | aconitate hydratase 1 |
| RA | 1,344,474 | G→T | 15.4% | intergenic (‑110/+34) | yciW ← / ← fabI | putative oxidoreductase/enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,422,040 | A→G | 13.2% | 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 | 15.5% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 5.3% | 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 | 6.5% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,452,826 | G→A | 8.0% | V102V (GTG→GTA) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,452,858 | C→T | 8.9% | A113V (GCA→GTA) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,460,421 | A→G | 6.3% | pseudogene (773/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,593 | C→G | 11.9% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,602 | T→C | 7.4% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,986 | G→A | 9.8% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,046 | C→T | 8.9% | pseudogene (1398/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,055 | A→G | 8.8% | pseudogene (1407/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,501,959 | A→G | 16.0% | I308V (ATT→GTT) | ydcP → | putative peptidase |
| RA | 1,516,587 | C→A | 7.0% | A246S (GCA→TCA) | yncD ← | putative iron outer membrane transporter |
| RA | 1,522,347 | T→C | 5.7% | pseudogene (189/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,529,506 | C→A | 15.5% | G204C (GGC→TGC) | yddE ← | PhzC‑PhzF family protein |
| RA | 1,542,906 | G→A | 12.1% | V417M (GTG→ATG) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,551,973 | C→A | 9.6% | W108L (TGG→TTG) | ddpF ← | D,D‑dipeptide permease system, ATP‑binding component |
| RA | 1,566,159 | G→A | 17.4% | D48D (GAC→GAT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,588,339 | T→G | 9.7% | pseudogene (3906/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,598,799 | C→T | 10.3% | P166S (CCG→TCG) | lsrD → | autoinducer 2 import system permease protein |
| RA | 1,652,888 | C→A | 7.8% | S188* (TCA→TAA) | ynfE → | putative selenate reductase, periplasmic |
| RA | 1,657,113 | G→T | 10.3% | A767A (GCG→GCT) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,660,041 | C→A | 10.3% | A157D (GCT→GAT) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,668,928 | G→A | 13.1% | L253L (CTG→CTA) | tqsA → | pheromone AI‑2 transporter |
| RA | 1,710,943 | C→A | 10.8% | Q179H (CAG→CAT) | tyrS ← | tyrosyl‑tRNA synthetase |
| RA | 1,713,419 | C→A | 8.9% | L147L (CTG→CTT) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,719,324 | G→T | 20.3% | P189Q (CCG→CAG) | ydhF ← | putative oxidoreductase |
| RA | 1,740,584 | G→A | 8.0% | intergenic (‑200/‑108) | ydhQ ← / → valV | autotransporter adhesin‑related protein/tRNA‑Val |
| RA | 1,884,412 | G→A | 11.8% | D126D (GAC→GAT) | yeaY ← | Slp family lipoprotein, RpoE‑regulated |
| RA | 1,904,057 | G→T | 10.7% | L100L (CTC→CTA) | kdgR ← | KDG regulon transcriptional repressor |
| RA | 1,942,126 | Δ1 bp | 12.9% | coding (283/741 nt) | yebC ← | UPF0082 family protein |
| JC JC | 1,972,762 | IS5 (–) +4 bp | 92.0% | intergenic (‑308/‑469) | flhD ← / → uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| RA | 1,979,631 | C→A | 14.3% | intergenic (‑22/‑775) | araF ← / → ftnB | L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir |
| RA | 2,014,421 | C→A | 9.5% | P285Q (CCG→CAG) | fliM → | flagellar motor switching and energizing component |
| RA | 2,031,744:1 | +A | 8.2% | coding (561/672 nt) | yedW ← | response regulator family protein |
| RA | 2,031,744:2 | +A | 8.2% | coding (561/672 nt) | yedW ← | response regulator family protein |
| RA | 2,031,745 | G→A | 8.2% | T187M (ACG→ATG) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,746 | T→G | 8.3% | T187P (ACG→CCG) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,748 | T→A | 8.4% | N186I (AAT→ATT) | yedW ← | response regulator family protein |
| RA | 2,031,752 | T→C | 8.4% | T185A (ACC→GCC) | yedW ← | response regulator family protein |
| RA | 2,031,753 | A→C | 7.3% | D184E (GAT→GAG) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,754 | T→G | 8.3% | D184A (GAT→GCT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,756 | A→T | 7.2% | S183R (AGT→AGA) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,757 | C→G | 6.8% | S183T (AGT→ACT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,759 | A→T | 6.8% | D182E (GAT→GAA) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,761 | C→T | 6.8% | D182N (GAT→AAT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,762 | A→C | 8.3% | F181L (TTT→TTG) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,763 | A→G | 8.4% | F181S (TTT→TCT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,764 | A→T | 8.3% | F181I (TTT→ATT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,766 | T→G | 8.5% | N180T (AAC→ACC) | yedW ← | response regulator family protein |
| RA | 2,031,768 | G→A | 8.5% | I179I (ATC→ATT) | yedW ← | response regulator family protein |
| RA | 2,031,771 | T→A | 8.2% | G178G (GGA→GGT) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,772:1 | +G | 8.5% | coding (533/672 nt) | yedW ← | response regulator family protein |
| RA | 2,031,773 | C→A | 8.5% | G178* (GGA→TGA) ‡ | yedW ← | response regulator family protein |
| RA | 2,031,779 | T→A | 8.5% | I176F (ATT→TTT) | yedW ← | response regulator family protein |
| RA | 2,112,080 | G→A | 25.0% | intergenic (‑195/+81) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,112,082 | T→A | 25.0% | intergenic (‑197/+79) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,112,118 | T→C | 22.7% | intergenic (‑233/+43) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,115,873:1 | +A | 11.4% | coding (588/1371 nt) | cpsG ← | phosphomannomutase |
| RA | 2,115,875 | G→A | 12.1% | L196F (CTC→TTC) | cpsG ← | phosphomannomutase |
| RA | 2,115,876 | G→T | 12.1% | A195A (GCC→GCA) | cpsG ← | phosphomannomutase |
| RA | 2,128,950 | C→A | 15.0% | V62L (GTA→TTA) | wzc ← | colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase |
| RA | 2,231,314 | G→A | 16.7% | S485S (TCC→TCT) | mglA ← | fused methyl‑galactoside transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 2,265,703 | C→A | 13.7% | P500Q (CCG→CAG) | rtn → | resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 2,274,261 | C→A | 17.6% | R51S (CGC→AGC) | yejH → | putative ATP‑dependent DNA or RNA helicase |
| RA | 2,279,085 | G→T | 8.7% | A411S (GCA→TCA) | yejM → | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| RA | 2,283,668 | C→A | 11.1% | intergenic (‑9/‑311) | yejO ← / → narP | pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system/response regulator in two‑component regulatory system with NarQ or NarX |
| RA | 2,296,302 | C→A | 7.5% | R64L (CGC→CTC) | napD ← | assembly protein for periplasmic nitrate reductase |
| RA | 2,347,550 | C→T | 6.0% | C475C (TGC→TGT) | glpA → | sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding |
| RA | 2,363,797 | C→T | 7.6% | H101Y (CAC→TAC) | arnD → | undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase |
| RA | 2,409,990 | Δ1 bp | 6.2% | coding (1765/2145 nt) | pta → | phosphate acetyltransferase |
| RA | 2,409,991 | Δ1 bp | 6.2% | coding (1766/2145 nt) | pta → | phosphate acetyltransferase |
| RA | 2,410,829 | G→C | 9.3% | P90P (CCG→CCC) | yfcC → | putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family |
| RA | 2,425,188 | C→T | 6.6% | E412K (GAA→AAA) | folC ← | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase |
| RA | 2,430,432 | A→C | 6.4% | L300R (CTG→CGG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,432,239 | C→A | 6.4% | Q271K (CAG→AAG) | flk → | putative flagella assembly protein |
| RA | 2,517,920 | C→T | 7.8% | L106L (CTG→CTA) | xapA ← | purine nucleoside phosphorylase II |
| RA | 2,549,244 | C→T | 6.7% | Q172Q (CAG→CAA) | eutL ← | putative ethanol utilization carboxysome structural protein |
| RA | 2,556,191 | C→A | 10.8% | R103R (CGC→CGA) | yffP → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,558,698 | C→T | 7.3% | intergenic (+7/+142) | yffS → / ← eutA | CPZ‑55 prophage; uncharacterized protein/reactivating factor for ethanolamine ammonia lyase |
| RA | 2,570,495 | G→A | 8.0% | D414D (GAC→GAT) | maeB ← | malic enzyme: putative oxidoreductase/putative phosphotransacetylase |
| RA | 2,585,803 | C→A | 9.8% | L280M (CTG→ATG) | dapE → | N‑succinyl‑diaminopimelate deacylase |
| RA | 2,598,736 | G→T | 7.0% | Q189H (CAG→CAT) | hyfD → | hydrogenase 4, membrane subunit |
| RA | 2,632,071 | G→A | 10.3% | P191L (CCG→CTG) | yfgM ← | putative anti‑RcsB factor |
| RA | 2,654,017 | C→A | 7.4% | D292Y (GAC→TAC) | iscS ← | cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent |
| RA | 2,677,571 | G→T | 6.6% | intergenic (+156/+42) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,709,141 | C→A | 14.1% | I120I (ATC→ATA) | eamB → | cysteine and O‑acetylserine exporter |
| RA | 2,724,771 | C→T | 14.8% | intergenic (‑255/+188) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,726,574 | C→T | 6.8% | R320H (CGC→CAC) | clpB ← | protein disaggregation chaperone |
| RA | 2,727,672 | C→A | 15.4% | W241L (TGG→TTG) | yfiH ← | UPF0124 family protein |
| RA | 2,762,455 | T→C | 15.7% | D144D (GAT→GAC) | yfjQ → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,771,529 | T→C | 19.6% | V1519V (GTA→GTG) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,771,561 | T→C | 11.5% | S1509G (AGT→GGT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,779,130 | T→C | 19.0% | noncoding (67/76 nt) | ileY ← | tRNA‑Ile |
| RA | 2,838,435 | G→T | 8.5% | P466T (CCG→ACG) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,848,074 | G→T | 7.5% | A126A (GCG→GCT) | fhlA → | formate hydrogenlyase transcriptional activator |
| RA | 2,913,548 | G→T | 7.4% | A186A (GCC→GCA) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 3,060,168 | G→A | 9.5% | T122I (ACC→ATC) | ygfI ← | putative DNA‑binding transcriptional regulator |
| RA | 3,075,123 | G→T | 6.5% | intergenic (‑129/‑149) | tktA ← / → loiP | transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era |
| RA | 3,075,535 | G→A | 6.4% | P88P (CCG→CCA) | loiP → | Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era |
| RA | 3,147,307 | G→C | 10.8% | G129A (GGA→GCA) ‡ | yghB → | general envelope maintenance protein; DedA family inner membrane protein |
| RA | 3,147,308 | A→G | 10.8% | G129G (GGA→GGG) ‡ | yghB → | general envelope maintenance protein; DedA family inner membrane protein |
| RA | 3,197,117 | G→A | 16.0% | A125V (GCG→GTG) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,211,130 | Δ1 bp | 7.7% | coding (1306/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,131 | Δ1 bp | 7.7% | coding (1305/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,132 | Δ1 bp | 7.7% | coding (1304/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,133 | Δ1 bp | 7.7% | coding (1303/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,134 | Δ1 bp | 7.7% | coding (1302/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,211,135 | Δ1 bp | 7.7% | coding (1301/1521 nt) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,218,158 | C→A | 10.8% | R723S (CGT→AGT) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,253,803 | G→A | 10.3% | L659L (CTG→TTG) | tdcE ← | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
| RA | 3,320,871 | C→T | 9.3% | P51P (CCG→CCA) | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,380,156 | G→A | 9.8% | S464S (AGC→AGT) | aaeB ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,416,890 | T→G | 23.0% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 30.1% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,455,859 | C→G | 8.0% | R53G (CGC→GGC) | gspJ → | putative general secretory pathway component, cryptic |
| RA | 3,476,745 | G→T | 10.3% | W62L (TGG→TTG) | yheT → | UPF0017 family putative hydrolase |
| RA | 3,478,310 | G→T | 5.7% | V154V (GTG→GTT) | prkB → | putative phosphoribulokinase |
| RA | 3,479,572 | C→A | 9.3% | H32N (CAC→AAC) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,500,191 | G→T | 8.9% | R169S (CGT→AGT) | yhfT ← | inner membrane protein |
| RA | 3,554,251 | C→A | 14.0% | V188L (GTG→TTG) | glpG ← | rhomboid intramembrane serine protease |
| RA | 3,559,529 | G→T | 12.1% | A138E (GCG→GAG) | glgP ← | glycogen phosphorylase |
| RA | 3,567,175 | G→A | 7.7% | A355V (GCC→GTC) | asd ← | aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding |
| RA | 3,570,962 | C→A | 18.7% | intergenic (‑10/+129) | gntK ← / ← gntR | gluconate kinase 2/d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,587,917 | C→A | 8.1% | P308P (CCG→CCT) | livM ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,614,361 | G→A | 9.4% | A604T (GCC→ACC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,615,943 | A→G | 10.2% | N1131S (AAC→AGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,615,959 | G→A | 8.3% | V1136V (GTG→GTA) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,061 | T→C | 5.8% | Y1170Y (TAT→TAC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,121 | G→C | 8.3% | R1190R (CGG→CGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,637,596 | A→G | 7.3% | L316S (TTG→TCG) | prlC ← | oligopeptidase A |
| RA | 3,664,231 | C→T | 6.1% | A427V (GCG→GTG) | treF → | cytoplasmic trehalase |
| RA | 3,671,592:1 | +C | 15.0% | coding (119/2061 nt) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,671,593:1 | +T | 15.0% | coding (118/2061 nt) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,673,567 | C→A | 9.5% | G263G (GGC→GGA) | kdgK → | 2‑dehydro‑3‑deoxygluconokinase |
| RA | 3,684,890 | C→A | 9.3% | A360S (GCG→TCG) | bcsB ← | regulator of cellulose synthase, cyclic di‑GMP binding |
| RA | 3,723,421 | C→T | 6.0% | P235P (CCG→CCA) | xylA ← | D‑xylose isomerase |
| RA | 3,729,074 | G→T | 35.7% | A246S (GCG→TCG) | xylR → | xylose divergent operon transcriptional activator |
| RA | 3,758,971 | C→T | 7.0% | I1143I (ATC→ATT) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,767,790 | G→C | 6.0% | A3P (GCA→CCA) | mtlD → | mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,768,492 | G→T | 12.1% | D237Y (GAC→TAC) | mtlD → | mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| RA | 3,843,955 | C→A | 9.1% | P44P (CCG→CCT) | uhpA ← | response regulator in two‑component regulatory system wtih UhpB |
| RA | 3,852,205 | C→A | 9.1% | M424I (ATG→ATT) | yidK ← | putative transporter |
| RA | 3,888,770 | A→G | 80.5% | I400I (ATT→ATC) | purP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,902,201 | G→A | 7.1% | A200V (GCG→GTG) | pstA ← | phosphate transporter subunit |
| RA | 3,904,265 | C→A | 8.7% | A207A (GCG→GCT) | pstS ← | periplasmic phosphate binding protein, high‑affinity |
| RA | 3,905,827 | G→T | 9.2% | A401E (GCA→GAA) | glmS ← | L‑glutamine:D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,911,235 | C→A | 9.3% | G131C (GGC→TGC) | atpG ← | F1 sector of membrane‑bound ATP synthase, gamma subunit |
| RA | 3,917,404 | G→T | 14.8% | A530A (GCC→GCA) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,923,307 | C→A | 10.0% | E383* (GAG→TAG) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,928,122 | A→G | 17.1% | I329V (ATT→GTT) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,928,123:1 | +C | 17.6% | coding (986/1506 nt) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,928,123:2 | +A | 17.6% | coding (986/1506 nt) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,928,123:3 | +G | 17.6% | coding (986/1506 nt) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,928,123:4 | +A | 17.6% | coding (986/1506 nt) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,993,478 | G→T | 11.1% | A712A (GCG→GCT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,018,574 | G→A | 11.1% | G76D (GGC→GAC) | ubiD → | 3‑octaprenyl‑4‑hydroxybenzoate decarboxylase |
| RA | 4,020,243 | C→A | 7.9% | R119R (CGC→CGA) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,028,635 | A→G | 36.4% | intergenic (+122/‑256) | hemG → / → rrsA | protoporphyrin oxidase, flavoprotein/16S ribosomal RNA of rrnA operon |
| RA | 4,058,149 | G→T | 8.1% | F326L (TTC→TTA) | yihO ← | putative transporter |
| RA | 4,108,892 | C→A | 10.0% | G123C (GGC→TGC) | rraA ← | ribonuclease E (RNase E) inhibitor protein |
| RA | 4,114,164 | Δ1 bp | 10.0% | coding (221/1026 nt) | cytR ← | Anti‑activator for CytR‑CRP nucleoside utilization regulon |
| RA | 4,132,480 | T→C | 20.0% | L8P (CTG→CCG) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,139,806 | C→T | 5.5% | A130T (GCC→ACC) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,143,982 | G→A | 6.8% | P265L (CCG→CTG) | argE ← | acetylornithine deacetylase |
| RA | 4,161,576 | A→C | 9.6% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,172,424 | G→T | 13.4% | G418C (GGT→TGT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,178,209 | C→T | 16.8% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 30.9% | R1075C (CGT→TGT) ‡ | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,501 | G→C | 40.5% | R1075P (CGT→CCT) ‡ | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,216,925 | A→G | 6.3% | Y1057C (TAC→TGC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,292,770 | C→T | 9.6% | L42L (CTG→CTA) | mdtO ← | membrane translocase (MDR) of MdtNOP efflux pump, PET family |
| RA | 4,308,243 | G→A | 7.1% | T113T (ACC→ACT) | phnK ← | carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein |
| RA | 4,314,866 | C→A | 6.1% | S39S (TCG→TCT) | phnC ← | phosphonate ABC transporter ATP‑binding subunit |
| RA | 4,336,238 | A→G | 15.1% | R302R (CGT→CGC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,241 | G→A | 15.1% | I301I (ATC→ATT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,244 | A→C | 12.1% | V300V (GTT→GTG) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,250 | A→G | 13.1% | I298I (ATT→ATC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,347,989 | G→T | 6.7% | T149N (ACT→AAT) | cadA ← | lysine decarboxylase, acid‑inducible |
| RA | 4,374,342 | G→T | 17.9% | L229L (CTG→CTT) | yjeM → | putative transporter |
| RA | 4,387,514 | G→T | 7.9% | G96C (GGT→TGT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,407,369 | Δ1 bp | 6.6% | coding (601/750 nt) | yjfP → | acyl CoA esterase |
| RA | 4,465,050 | G→T | 9.3% | P124P (CCG→CCT) | tabA → | biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily |
| RA | 4,502,929 | C→A | 8.9% | G100C (GGC→TGC) | fecC ← | iron‑dicitrate transporter subunit |
| RA | 4,513,876 | G→A | 9.1% | H12H (CAC→CAT) | yjhG ← | putative dehydratase |
| RA | 4,552,151 | C→A | 13.2% | L114L (CTG→CTT) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| RA | 4,578,481 | A→G | 5.2% | S68P (TCG→CCG) | yjiA ← | GTP‑binding protein, putative GTPase |
| RA | 4,583,011 | C→T | 9.1% | A513V (GCA→GTA) | tsr → | methyl‑accepting chemotaxis protein I, serine sensor receptor |
| RA | 4,594,789 | G→A | 6.8% | T231I (ACC→ATC) | fhuF ← | ferric iron reductase involved in ferric hydroximate transport |
| RA | 4,604,485 | G→A | 6.8% | intergenic (+408/+12) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 80439 | 80632 | 194 | 4 [3] | [2] 4 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | CP009273 | 454338 | 456505 | 2168 | 12 [2] | [2] 4 | [lon] | [lon] |
| * | * | ÷ | CP009273 | 578896 | 579075 | 180 | 4 [3] | [3] 5 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 766262 | 766438 | 177 | 5 [3] | [3] 4 | mngB/cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| * | * | ÷ | CP009273 | 1294723 | 1294732 | 10 | 6 [1] | [0] 6 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| * | * | ÷ | CP009273 | 1524324 | 1524473 | 150 | 6 [3] | [2] 5 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 2027284 | 2027397 | 114 | 4 [3] | [3] 5 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2462808 | 2462909 | 102 | 6 [3] | [2] 4 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463554 | 2463776 | 223 | 6 [2] | [3] 4 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2988537 | 2988683 | 147 | 4 [2] | [1] 4 | [ygeN] | [ygeN] |
| * | * | ÷ | CP009273 | 3448799 | 3448865 | 67 | 5 [2] | [1] 8 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3792595 | 3792905 | 311 | 8 [2] | [2] 7 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | CP009273 | 3798102 | 3798404 | 303 | 5 [2] | [3] 4 | waaS | lipopolysaccharide core biosynthesis protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 33 (0.910) | 33 (0.910) | 22/250 | NT | 50.0% | 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 | 1203246 = | 17 (0.470) | 13 (0.410) | 9/218 | NT | 59.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 3 (0.090) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 17 (0.470) | 22 (0.700) | 7/218 | NT | 71.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 3 (0.090) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2399639 | 44 (1.210) | 4 (0.110) | 4/250 | NT | 8.3% | 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 | |||||