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 | 30,387 | C→T | 8.4% | A246V (GCC→GTC) | carA → | carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| RA | 65,142 | G→T | 5.9% | A213A (GCC→GCA) | polB ← | DNA polymerase II |
| RA | 90,927 | C→A | 5.4% | I425I (ATC→ATA) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase |
| RA | 200,626 | G→T | 6.6% | A264A (GCG→GCT) | lpxB → | tetraacyldisaccharide‑1‑P synthase |
| RA | 221,173 | T→G | 6.4% | noncoding (916/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 235,640 | C→T | 7.0% | pseudogene (48/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 247,164 | C→T | 5.2% | pseudogene (606/756 nt) | lafU → | pseudogene, lateral flagellar motor protein fragment |
| RA | 249,531 | C→T | 11.4% | S112S (AGC→AGT) | yafP → | putative acyl‑CoA transferase |
| RA | 305,573 | G→T | 8.5% | L55L (CTC→CTA) | ecpB ← | ECP production pilus chaperone |
| RA | 390,847 | C→A | 6.1% | M299I (ATG→ATT) | ampH ← | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase |
| RA | 404,893 | C→A | 6.1% | A195S (GCC→TCC) | rdgC ← | nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function |
| RA | 472,858 | C→A | 8.6% | A406S (GCC→TCC) | ylaB ← | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 476,240 | C→A | 6.9% | intergenic (‑76/+470) | tomB ← / ← acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| RA | 497,707 | Δ1 bp | 8.3% | coding (988/1677 nt) | ybaL ← | inner membrane putative NAD(P)‑binding transporter |
| RA | 499,294 | C→A | 6.2% | G287W (GGG→TGG) | fsr ← | putative fosmidomycin efflux system protein |
| RA | 516,006 | G→A | 5.2% | Q45Q (CAG→CAA) | ybbP → | putative ABC transporter permease |
| RA | 516,173 | C→T | 6.2% | A101V (GCG→GTG) | ybbP → | putative ABC transporter permease |
| RA | 576,565 | G→A | 10.0% | A92A (GCG→GCA) | nohD → | DLP12 prophage; DNA packaging protein |
| RA | 578,457 | C→A | 8.4% | pseudogene (49/183 nt) | tfaX → | pseudogene, DLP12 prophage;Phage or Prophage Related |
| RA | 589,708 | G→T | 5.2% | I173I (ATC→ATA) | cusS ← | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
| RA | 682,808 | C→A | 13.7% | V132V (GTG→GTT) | gltI ← | glutamate, aspartate binding protein, periplasmic; part of GltJKLI ABC transporter |
| RA | 727,989 | C→A | 6.6% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,083 | G→A | 13.0% | pseudogene (495/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 731,020 | C→A | 5.9% | pseudogene (1432/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 757,509 | C→T | 7.1% | R178C (CGT→TGT) | sucB → | dihydrolipoyltranssuccinase |
| RA | 811,085 | T→C | 7.5% | intergenic (+82/+110) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,094 | T→G | 10.2% | intergenic (+91/+101) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,095 | G→A | 8.2% | intergenic (+92/+100) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,096 | C→T | 8.8% | intergenic (+93/+99) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,097 | G→A | 14.9% | intergenic (+94/+98) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,099:1 | +A | 8.0% | intergenic (+96/+96) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 832,455 | C→A | 6.7% | P217T (CCG→ACG) | ybiC → | putative dehydrogenase |
| RA | 875,194 | C→A | 7.7% | R333S (CGT→AGT) | yliI → | soluble aldose sugar dehydrogenase |
| RA | 894,952 | C→A | 5.7% | R327S (CGT→AGT) | rlmC → | 23S rRNA m(5)U747 methyltransferase, SAM‑dependent |
| RA | 955,928 | C→A | 9.5% | S70Y (TCC→TAC) | ycaL → | putative peptidase‑related chaperone |
| RA | 968,382 | A→G | 8.9% | L159P (CTG→CCG) | ycbC ← | DUF218 superfamily protein |
| RA | 1,015,272 | C→A | 8.3% | G80C (GGT→TGT) | ompA ← | outer membrane protein A (3a;II*;G;d) |
| RA | 1,020,310 | G→A | 6.4% | V128V (GTG→GTA) | helD → | DNA helicase IV |
| RA | 1,024,891 | G→A | 5.6% | P179S (CCA→TCA) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,026,023 | Δ1 bp | 5.6% | coding (102/330 nt) | tusE ← | mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 1,036,640 | C→T | 6.4% | R190W (CGG→TGG) | appA → | phosphoanhydride phosphorylase |
| RA | 1,107,318 | C→A | 9.8% | R334S (CGC→AGC) | opgH → | membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,150,703 | G→A | 5.8% | G42S (GGC→AGC) | tmk → | thymidylate kinase |
| RA | 1,158,400 | C→A | 6.2% | L103M (CTG→ATG) | lpoB → | OM lipoprotein stimulator of MrcB transpeptidase |
| RA | 1,161,072 | G→A | 5.4% | E158E (GAG→GAA) | ycfP → | putative UPF0227 family esterase |
| RA | 1,196,044 | C→A | 6.1% | R73S (AGG→AGT) | intE ← | e14 prophage; putative integrase |
| RA | 1,205,973 | C→A | 12.2% | Q58K (CAA→AAA) | mcrA → | putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene |
| RA | 1,239,619 | G→T | 8.0% | P122Q (CCA→CAA) | ycgR ← | flagellar velocity braking protein, c‑di‑GMP‑regulated |
| RA | 1,275,217 | G→T | 7.7% | intergenic (+413/‑103) | narK → / → narG | nitrate/nitrite transporter/nitrate reductase 1, alpha subunit |
| RA | 1,297,709 | A→T | 9.8% | Y185F (TAT→TTT) | oppB → | oligopeptide transporter subunit |
| RA | 1,298,848 | G→A | 7.4% | S253N (AGC→AAC) | oppC → | oligopeptide transporter subunit |
| RA | 1,381,352 | G→A | 12.1% | A126T (GCA→ACA) | tyrR → | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| RA | 1,383,810 | G→T | 7.9% | Q208H (CAG→CAT) | ycjG → | L‑Ala‑D/L‑Glu epimerase |
| RA | 1,386,463 | C→A | 9.1% | G72G (GGC→GGA) | pgrR → | murein peptide degradation regulator |
| RA | 1,417,567 | T→C | 12.2% | pseudogene (110/444 nt) | rzpR → | pseudogene, Rac prophage; Bacteriophage Rz lysis protein family;Phage or Prophage Related; putative Rac prophage endopeptidase; completely contained in another CDS |
| RA | 1,450,956 | G→T | 7.5% | Q90H (CAG→CAT) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| RA | 1,460,567 | A→G | 8.5% | pseudogene (919/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,593 | C→G | 9.5% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,602 | T→C | 13.8% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 11.1% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 10.8% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,887 | G→C | 15.8% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,896 | C→T | 17.6% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,479,744 | C→A | 13.2% | S809S (TCC→TCA) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,526,840 | G→A | 7.1% | G256G (GGG→GGA) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,526,876 | C→A | 9.8% | S268S (TCC→TCA) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,527,189 | A→G | 10.4% | T373A (ACG→GCG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,544,169 | A→C | 6.9% | I838L (ATC→CTC) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,172 | A→G | 7.1% | N839D (AAC→GAC) ‡ | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,174 | C→T | 7.2% | N839N (AAC→AAT) ‡ | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,177 | A→G | 7.3% | K840K (AAA→AAG) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,558,554 | G→A | 5.1% | S479S (AGC→AGT) | dosP ← | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| RA | 1,566,159 | G→A | 17.9% | D48D (GAC→GAT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,629,745 | T→A | 18.5% | A120A (GCA→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,656,947 | C→A | 6.4% | P712Q (CCA→CAA) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,702,047 | C→A | 10.4% | P291Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,963 | C→A | 7.2% | A596A (GCC→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,975 | G→A | 7.2% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,007 | A→T | 6.3% | E611V (GAA→GTA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,101 | C→G | 7.5% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,104 | G→A | 5.1% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,784,418 | G→T | 14.5% | R362S (CGC→AGC) | ydiU ← | UPF0061 family protein |
| RA | 1,857,199 | G→A | 10.0% | V58I (GTT→ATT) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,928,749 | G→T | 6.6% | S38* (TCG→TAG) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,965,923 | C→T | 6.2% | V342V (GTG→GTA) | tar ← | methyl‑accepting chemotaxis protein II |
| RA | 2,007,584 | C→T | 6.7% | S292L (TCA→TTA) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,027,811 | G→A | 7.5% | pseudogene (280/663 nt) | yedS → | pseudogene, outer membrane protein homology; putative outer membrane protein |
| RA | 2,102,959 | G→T | 10.3% | T36K (ACA→AAA) | wzxB ← | putative polisoprenol‑linked O‑antigen transporter |
| RA | 2,170,724 | G→T | 35.0% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,217,693:1 | +G | 5.4% | coding (657/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,698 | Δ1 bp | 5.9% | coding (652/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,699 | A→C | 5.9% | N217K (AAT→AAG) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,701 | T→A | 5.6% | N217Y (AAT→TAT) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,702 | A→C | 5.6% | T216T (ACT→ACG) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,703 | G→A | 5.6% | T216I (ACT→ATT) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,704 | T→C | 5.5% | T216A (ACT→GCT) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,707 | T→G | 5.5% | N215H (AAT→CAT) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,708:1 | +A | 5.6% | coding (642/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,709:1 | +A | 5.6% | coding (641/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,709:2 | +T | 5.6% | coding (641/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,710 | G→T | 5.5% | R214S (CGC→AGC) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,711 | G→C | 5.5% | F213L (TTC→TTG) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,712 | A→G | 5.3% | F213S (TTC→TCC) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,217,713 | A→T | 5.3% | F213I (TTC→ATC) ‡ | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,219,613 | C→T | 5.8% | L112L (CTG→TTG) | yohD → | DedA family inner membrane protein |
| RA | 2,304,935 | C→T | 8.7% | A27T (GCC→ACC) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| RA | 2,324,402 | G→T | 5.0% | pseudogene (3480/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,327,515 | C→A | 7.8% | pseudogene (367/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,333,809 | Δ1 bp | 5.1% | intergenic (+41/+87) | ubiG → / ← yfaL | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase/adhesin |
| RA | 2,378,895 | C→T | 7.3% | A103T (GCT→ACT) | yfbK ← | Von Willebrand factor domain putative lipoprotein |
| RA | 2,422,584 | C→A | 10.8% | Q378H (CAG→CAT) | purF ← | amidophosphoribosyltransferase |
| RA | 2,430,099 | C→A | 6.3% | L10L (CTG→CTT) | usg ← | putative semialdehyde dehydrogenase |
| RA | 2,528,734 | Δ1 bp | 5.9% | coding (1310/1728 nt) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,589,632 | C→A | 5.3% | A155A (GCG→GCT) | ypfJ ← | putative neutral zinc metallopeptidase |
| RA | 2,629,456 | C→A | 8.4% | V420V (GTG→GTT) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,633,390 | A→G | 7.7% | V182A (GTG→GCG) | hisS ← | histidyl tRNA synthetase |
| RA | 2,690,483 | G→T | 5.1% | E442* (GAA→TAA) | mltF → | membrane‑bound lytic transglycosylase F, murein hydrolase |
| RA | 2,719,426 | T→C | 8.2% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,724,437 | G→T | 5.8% | noncoding (80/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,776,112 | C→A | 5.6% | intergenic (‑27/+312) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| RA | 2,798,587 | C→A | 5.2% | A138A (GCC→GCA) | proV → | glycine betaine transporter subunit |
| RA | 2,815,353 | A→G | 13.3% | A6A (GCT→GCC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,824,415 | G→T | 8.4% | H412N (CAT→AAT) | norR ← | anaerobic nitric oxide reductase DNA‑binding transcriptional activator |
| RA | 2,887,576 | C→A | 5.3% | R8S (CGC→AGC) | ygcP → | putative antiterminator regulatory protein |
| RA | 2,895,606 | G→T | 8.5% | D118Y (GAC→TAC) | ygcE → | putative kinase |
| RA | 2,956,559 | G→A | 5.1% | Q173* (CAA→TAA) | ppdB ← | putative prepilin peptidase‑dependent protein |
| RA | 2,973,589 | C→A | 8.2% | G136W (GGG→TGG) | ygeA ← | Asp/Glu_racemase family protein |
| RA | 3,015,569 | C→T | 8.2% | P299S (CCG→TCG) | xdhD → | putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding |
| RA | 3,107,435 | C→A | 5.8% | D93Y (GAC→TAC) | pppA ← | bifunctional prepilin leader peptidase/ methylase |
| RA | 3,109,205:1 | +T | 5.7% | coding (3267/4563 nt) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,109,206 | C→G | 5.7% | W1089S (TGG→TCG) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,198,656 | A→G | 6.4% | K202E (AAG→GAG) | plsY → | putative glycerol‑3‑phosphate acyltransferase |
| RA | 3,209,603 | G→T | 5.0% | P83Q (CCA→CAA) | yqjH ← | putative siderophore interacting protein |
| RA | 3,233,343 | C→A | 5.3% | A14D (GCT→GAT) | sstT → | sodium:serine/threonine symporter |
| RA | 3,286,375 | C→T | 6.0% | R107H (CGT→CAT) | rsmI ← | 16S rRNA C1402 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,319,721 | C→T | 8.9% | G192S (GGT→AGT) | ftsH ← | protease, ATP‑dependent zinc‑metallo |
| RA | 3,340,030 | C→A | 5.1% | L32M (CTG→ATG) | ptsN → | sugar‑specific enzyme IIA component of PTS |
| RA | 3,416,890 | T→G | 8.0% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,433,794 | C→A | 36.8% | D199Y (GAC→TAC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,433,808 | T→G | 14.9% | Q194P (CAG→CCG) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,498,239 | A→C | 11.9% | intergenic (+97/+55) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,507,367 | G→T | 6.1% | L128M (CTG→ATG) | gph ← | phosphoglycolate phosphatase |
| RA | 3,532,208 | Δ1 bp | 6.1% | coding (1465/2322 nt) | yhgF → | putative transcriptional accessory protein |
| RA | 3,532,209 | Δ1 bp | 6.1% | coding (1466/2322 nt) | yhgF → | putative transcriptional accessory protein |
| RA | 3,532,210 | Δ1 bp | 5.7% | coding (1467/2322 nt) | yhgF → | putative transcriptional accessory protein |
| RA | 3,565,480 | G→T | 14.4% | T461T (ACC→ACA) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,586,364:1 | +A | 5.3% | coding (434/714 nt) | livF ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,586,364:2 | +G | 5.3% | coding (434/714 nt) | livF ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,586,364:3 | +T | 5.3% | coding (434/714 nt) | livF ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,634,512 | G→T | 5.3% | M97I (ATG→ATT) | dtpB → | dipeptide and tripeptide permease B |
| RA | 3,650,457 | G→T | 8.9% | G35W (GGG→TGG) | hdeD → | acid‑resistance membrane protein |
| RA | 3,717,109 | C→A | 7.2% | A217S (GCC→TCC) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,742,844 | C→A | 5.7% | R85S (CGT→AGT) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,819,715 | C→A | 7.7% | F382L (TTC→TTA) | recG → | ATP‑dependent DNA helicase |
| RA | 3,899,270 | C→A | 9.2% | A220S (GCT→TCT) | bglG ← | transcriptional antiterminator of the bgl operon |
| RA | 3,899,591 | C→T | 5.4% | V113M (GTG→ATG) | bglG ← | transcriptional antiterminator of the bgl operon |
| RA | 3,936,730 | C→A | 6.2% | intergenic (+21/‑65) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 4,040,278 | T→C | 10.0% | intergenic (‑316/‑48) | yihG ← / → polA | inner membrane protein, inner membrane acyltransferase/fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease |
| RA | 4,049,693 | T→C | 6.6% | T3A (ACA→GCA) | glnL ← | sensory histidine kinase in two‑component regulatory system with GlnG |
| RA | 4,071,150 | T→C | 6.6% | R114R (CGT→CGC) | yiiD → | putative acetyltransferase |
| RA | 4,091,025 | G→T | 5.3% | Q96H (CAG→CAT) | sodA → | superoxide dismutase, Mn |
| RA | 4,100,153 | A→G | 8.4% | N99S (AAC→AGC) | cdh → | CDP‑diacylglycerol phosphotidylhydrolase |
| RA | 4,125,079 | G→A | 5.7% | P439P (CCG→CCA) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,131,877 | G→A | 5.1% | C91C (TGC→TGT) | frwA ← | putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component |
| RA | 4,165,449 | C→T | 19.4% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 19.4% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,166,006 | C→T | 15.8% | R45R (CGC→CGT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,167,038 | A→T | 7.2% | V389V (GTA→GTT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,167,041 | A→T | 7.6% | A390A (GCA→GCT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,167,051 | A→G | 7.5% | S394G (AGC→GGC) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,177,142 | A→T | 5.3% | D622V (GAC→GTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,209 | C→T | 9.9% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,199,631 | T→A | 10.6% | intergenic (+15/‑71) | rrsE → / → gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu |
| RA | 4,215,580 | C→T | 5.8% | P609S (CCC→TCC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,289,072 | G→A | 5.3% | Q38* (CAG→TAG) | fdhF ← | formate dehydrogenase‑H, selenopolypeptide subunit |
| RA | 4,329,684 | C→A | 5.8% | G219C (GGT→TGT) | adiA ← | arginine decarboxylase |
| RA | 4,330,517 | G→T | 6.7% | intergenic (‑179/+20) | adiA ← / ← melR | arginine decarboxylase/melibiose operon transcriptional regulator; autoregulator |
| RA | 4,343,052 | C→T | 8.9% | V495I (GTT→ATT) | lysU ← | lysine tRNA synthetase, inducible |
| RA | 4,382,345 | G→T | 7.6% | noncoding (57/76 nt) | glyX → | tRNA‑Gly |
| RA | 4,400,970 | G→T | 6.9% | D201Y (GAC→TAC) | yjfJ → | PspA/IM30 family protein |
| RA | 4,432,075 | G→T | 11.1% | intergenic (‑82/‑124) | msrA ← / → tamA | methionine sulfoxide reductase A/translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,462,926 | G→T | 10.0% | S34Y (TCC→TAC) | yjgH ← | UPF0131 family protein |
| RA | 4,498,906 | T→C | 9.1% | pseudogene (81/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,909 | G→T | 9.5% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,533,877 | G→T | 11.1% | E111D (GAG→GAT) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,565,972 | G→A | 6.1% | pseudogene (2237/2937 nt) | yjiV → | pseudogene; conserved hypothetical protein |
| RA | 4,626,148 | C→A | 8.4% | R109S (CGC→AGC) | creB → | response regulator in two‑component regulatory system with CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 578865 | 579065 | 201 | 7 [6] | [6] 7 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 2050210 | 2050282 | 73 | 8 [6] | [6] 8 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
| * | * | ÷ | CP009273 | 2462825 | 2463233 | 409 | 8 [6] | [6] 7 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2988484 | 2988716 | 233 | 7 [6] | [6] 8 | [ygeN] | [ygeN] |
| * | * | ÷ | CP009273 | 3792468 | 3792906 | 439 | 7 [6] | [6] 7 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | CP009273 | 3797617 | 3798024 | 408 | 8 [3] | [5] 7 | waaS | lipopolysaccharide core biosynthesis protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 74 (1.130) | 90 (1.370) | 31/250 | NT | 54.9% | 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 = | 55 (0.840) | 11 (0.190) | 8/218 | NT | 25.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 15 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 55 (0.840) | 32 (0.560) | 13/218 | NT | 50.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 15 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 3196596 | NA (NA) | 4 (0.060) | 3/246 | NT | 8.3% | noncoding (94/125 nt) | REP225 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP225 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | CP009273 | 4206831 = | 44 (0.680) | coding (1426/1602 nt) | aceB | malate synthase A | |||||