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 | 23,923 | C→A | 9.4% | L511L (CTC→CTA) | ileS → | isoleucyl‑tRNA synthetase |
| RA | 154,164:1 | +C | 17.1% | coding (56/480 nt) | folK ← | 2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase |
| RA | 203,315 | C→T | 18.2% | A568V (GCG→GTG) | dnaE → | DNA polymerase III alpha subunit |
| RA | 235,604 | A→T | 12.0% | pseudogene (12/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 235,610 | G→A | 11.8% | pseudogene (18/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 235,622 | A→G | 12.0% | pseudogene (30/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 236,251 | G→A | 7.7% | Y142Y (TAC→TAT) | yafV ← | putative NAD(P)‑binding C‑N hydrolase family amidase |
| RA | 259,937 | T→G | 5.9% | R8R (AGG→CGG) | ykfH ← | uncharacterized protein |
| RA | 266,165 | C→A | 11.1% | pseudogene (177/258 nt) | insN → | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 267,666 | C→T | 5.8% | pseudogene (192/426 nt) | insN → | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 286,409 | T→A | 11.4% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 310,768 | C→A | 15.1% | pseudogene (701/872 nt) | eaeH → | pseudogene, attaching and effacing protein homology;factor; Not classified |
| RA | 318,632 | A→G | 9.8% | D195G (GAT→GGT) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 419,377 | C→A | 8.6% | V468V (GTC→GTA) | malZ → | maltodextrin glucosidase |
| RA | 421,095 | G→T | 10.6% | G210V (GGC→GTC) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | 456,349 | C→T | 12.9% | P669L (CCG→CTG) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 458,905 | C→A | 9.6% | A512D (GCC→GAC) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 519,282 | C→G | 5.8% | S189C (TCT→TGT) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 638,794 | G→T | 12.5% | intergenic (+12/+219) | ybdR → / ← rnk | putative Zn‑dependent NAD(P)‑binding oxidoreductase/regulator of nucleoside diphosphate kinase |
| RA | 681,714 | G→T | 9.5% | P138T (CCG→ACG) | gltJ ← | glutamate, aspartate ABC transporter permease subunit |
| RA | 726,100 | A→G | 12.7% | R354R (CGA→CGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,406 | C→A | 5.6% | I456I (ATC→ATA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,453 | G→A | 6.2% | S472N (AGC→AAC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,830 | G→A | 12.3% | A598T (GCC→ACC) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,831 | C→T | 9.1% | A598V (GCC→GTC) ‡ | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,848 | A→G | 7.4% | T604A (ACC→GCC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,207 | C→T | 9.0% | R723R (CGC→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,555 | A→C | 7.8% | pseudogene (967/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 732,071 | T→C | 12.1% | pseudogene (171/240 nt) | ybfQ → | pseudogene, H repeat‑associated protein |
| RA | 733,602 | G→A | 9.0% | A19T (GCC→ACC) | ybfD → | H repeat‑associated putative transposase |
| RA | 752,090 | C→A | 6.2% | P243Q (CCG→CAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 791,151 | G→T | 15.4% | G203W (GGG→TGG) | modA → | molybdate transporter subunit |
| RA | 793,168 | C→A | 12.0% | M240I (ATG→ATT) | ybhA ← | pyridoxal phosphate (PLP) phosphatase |
| RA | 845,563 | C→A | 14.8% | intergenic (‑10/‑343) | rhtA ← / → ompX | threonine and homoserine efflux system/outer membrane protein X |
| RA | 939,824 | G→T | 11.1% | P112P (CCG→CCT) | dmsC → | dimethyl sulfoxide reductase, anaerobic, subunit C |
| RA | 948,489 | G→A | 9.8% | G174G (GGC→GGT) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 1,044,051 | C→A | 9.8% | E33* (GAA→TAA) | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,045,283 | T→G | 15.9% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,099,592 | G→T | 8.2% | Q62H (CAG→CAT) | csgB → | curlin nucleator protein, minor subunit in curli complex |
| RA | 1,231,137 | C→A | 20.0% | intergenic (+24/+28) | fadR → / ← ycgB | fatty acid metabolism regulon transcriptional regulator/SpoVR family stationary phase protein |
| RA | 1,265,353 | T→G | 6.0% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,282,243 | G→A | 9.0% | intergenic (+261/+279) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,421 | A→G | 11.3% | 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 | 12.2% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,439 | A→G | 9.9% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,455 | Δ1 bp | 10.3% | intergenic (+473/+67) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,608 | T→C | 6.9% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,291,629 | C→A | 12.3% | G650V (GGT→GTT) | adhE ← | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| RA | 1,313,723 | G→T | 10.8% | A108D (GCC→GAC) | trpC ← | fused indole‑3‑glycerolphosphate synthetase/N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,332,470 | G→A | 12.0% | A795T (GCC→ACC) | acnA → | aconitate hydratase 1 |
| RA | 1,342,483 | G→T | 11.4% | A229A (GCC→GCA) | rnb ← | ribonuclease II |
| RA | 1,351,794 | C→A | 10.9% | M44I (ATG→ATT) | ymjA ← | DUF2543 family protein |
| RA | 1,375,196 | G→T | 8.5% | pseudogene (119/957 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,419,700 | A→G | 6.5% | R23G (AGG→GGG) | ynaK → | Rac prophage; conserved protein |
| RA | 1,422,098 | G→A | 8.7% | pseudogene (886/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,150 | C→T | 5.2% | pseudogene (834/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 7.5% | 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 | 6.1% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,491,796 | C→A | 11.4% | T228T (ACC→ACA) | opgD → | osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein |
| RA | 1,510,726 | G→T | 8.7% | E298* (GAA→TAA) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,522,374 | C→T | 6.6% | pseudogene (216/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,523,601 | G→A | 10.8% | pseudogene (1443/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,523,604 | G→A | 11.1% | pseudogene (1446/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,527,173 | C→T | 9.1% | Y367Y (TAC→TAT) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,527,189 | A→G | 15.8% | T373A (ACG→GCG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,542,224 | A→C | 12.8% | V189V (GTA→GTC) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,543,556 | G→A | 7.4% | L633L (TTG→TTA) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,543,952 | G→T | 10.5% | L765L (CTG→CTT) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,566,159 | G→A | 18.2% | D48D (GAC→GAT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,615,208 | C→A | 25.0% | G63W (GGG→TGG) | eamA ← | cysteine and O‑acetyl‑L‑serine efflux system |
| RA | 1,616,734 | A→G | 11.9% | K382K (AAA→AAG) | ydeE → | putative transporter |
| RA | 1,741,170 | C→A | 20.1% | R72R (CGA→AGA) | ydhR → | putative monooxygenase |
| RA | 1,763,732 | G→A | 7.4% | G134G (GGG→GGA) | ydiK → | UPF0118 family inner membrane protein |
| RA | 1,776,264 | G→T | 8.3% | E205* (GAG→TAG) | ydiS → | putative oxidoreductase |
| RA | 1,825,672 | C→A | 10.5% | E190* (GAA→TAA) | astC ← | succinylornithine transaminase, PLP‑dependent |
| RA | 1,838,490 | A→G | 12.5% | N213N (AAT→AAC) | ynjI ← | inner membrane protein |
| RA | 1,946,243 | A→G | 6.5% | I198V (ATC→GTC) | yecE → | UPF0759 family protein |
| RA | 1,966,144 | G→A | 8.0% | R269C (CGC→TGC) | tar ← | methyl‑accepting chemotaxis protein II |
| RA | 2,067,642 | C→A | 8.7% | L875M (CTG→ATG) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,068,063 | C→T | 5.5% | A1015V (GCC→GTC) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,073,561 | C→T | 17.1% | R171H (CGC→CAC) | yeeA ← | putative transporter, FUSC family inner membrane protein |
| RA | 2,093,456 | G→T | 12.9% | R432S (CGT→AGT) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,194,165 | Δ1 bp | 8.9% | coding (408/3633 nt) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,215,467 | A→G | 10.2% | M1T (ATG→ACG) † | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,242,953 | G→A | 16.0% | L49L (CTG→TTG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,286,143 | C→A | 10.6% | V101F (GTC→TTC) | dsbE ← | periplasmic thioredoxin of cytochrome c‑type biogenesis |
| RA | 2,298,277 | T→C | 8.3% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,326,086 | C→A | 7.2% | pseudogene (1796/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,331,055 | G→A | 7.5% | R615R (CGC→CGT) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,355,130 | G→A | 32.0% | G187G (GGC→GGT) | rhmR ← | putative DNA‑binding transcriptional regulator for the rhm operon |
| RA | 2,367,615 | C→A | 7.3% | G290C (GGT→TGT) | menE ← | O‑succinylbenzoate‑CoA ligase |
| RA | 2,372,654 | C→T | 17.4% | A29T (GCC→ACC) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,385,510 | G→A | 7.5% | A337A (GCC→GCT) | nuoM ← | NADH:ubiquinone oxidoreductase, membrane subunit M |
| RA | 2,386,739 | G→A | 12.5% | A596V (GCA→GTA) | nuoL ← | NADH:ubiquinone oxidoreductase, membrane subunit L |
| RA | 2,389,651 | G→T | 11.2% | R93R (CGC→CGA) | nuoI ← | NADH:ubiquinone oxidoreductase, chain I |
| RA | 2,390,812 | C→T | 8.9% | R37H (CGT→CAT) | nuoH ← | NADH:ubiquinone oxidoreductase, membrane subunit H |
| RA | 2,410,852 | A→G | 10.8% | E98G (GAA→GGA) | yfcC → | putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family |
| RA | 2,432,260 | C→A | 7.3% | Q278K (CAG→AAG) | flk → | putative flagella assembly protein |
| RA | 2,555,743 | G→A | 6.1% | V92I (GTC→ATC) | yffO → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,596,740 | C→T | 10.2% | P522S (CCC→TCC) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,606,516 | G→T | 7.8% | D420Y (GAC→TAC) | hyfR → | hydrogenase‑4 transcriptional activator |
| RA | 2,654,663 | G→T | 16.1% | T76T (ACC→ACA) | iscS ← | cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent |
| RA | 2,719,426 | T→C | 80.7% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,761,782 | G→T | 6.7% | Q238H (CAG→CAT) | yfjP → | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,765,683 | A→C | 11.3% | pseudogene (743/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,765,687 | G→C | 12.0% | pseudogene (739/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,765,688 | G→T | 12.0% | pseudogene (738/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,773,187 | G→A | 5.8% | Q967* (CAG→TAG) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,784,120 | C→T | 7.0% | I260I (ATC→ATT) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,821,290 | G→A | 7.3% | E65E (GAG→GAA) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,823,219 | G→A | 7.2% | E16E (GAG→GAA) | srlQ → | D‑arabinose 5‑phosphate isomerase |
| RA | 2,828,862 | C→A | 8.7% | V641V (GTG→GTT) | hypF ← | carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases |
| RA | 2,838,330 | C→T | 6.9% | A501T (GCG→ACG) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,910,464 | C→A | 22.7% | I683I (ATC→ATA) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,920,857 | G→T | 13.8% | A397A (GCG→GCT) | ygdH → | UPF0717 family protein |
| RA | 2,940,824 | Δ1 bp | 13.8% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,940,826 | A→C | 19.1% | intergenic (+4/‑30) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,957,216 | C→A | 10.3% | L107L (CTG→CTT) | ppdA ← | putative prepilin peptidase‑dependent protein |
| RA | 3,012,612 | C→T | 8.0% | V31V (GTC→GTT) | ssnA → | putative chlorohydrolase/aminohydrolase |
| RA | 3,037,885 | C→A | 6.5% | R289S (CGT→AGT) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,064,718 | T→G | 18.1% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,070,336 | G→T | 10.5% | H160Q (CAC→CAA) | yggP ← | putative Zn‑binding dehydrogenase |
| RA | 3,120,743 | G→T | 10.3% | S213* (TCG→TAG) | glcD ← | glycolate oxidase subunit, FAD‑linked |
| RA | 3,195,411 | G→A | 5.9% | T54T (ACG→ACA) | cca → | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase |
| RA | 3,202,613 | G→A | 5.6% | A411T (GCT→ACT) | ttdT → | L‑tartrate/succinate antiporte |
| RA | 3,234,184 | G→T | 5.8% | L294L (CTG→CTT) | sstT → | sodium:serine/threonine symporter |
| RA | 3,252,730 | G→A | 7.8% | S93S (AGC→AGT) | tdcG ← | L‑serine dehydratase 3, anaerobic |
| RA | 3,263,502 | C→T | 14.3% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,274,855 | G→A | 6.4% | pseudogene (426/555 nt) | agaA → | pseudogene, N‑acetylgalactosamine‑6‑phosphate deacetylase fragment; putative N‑acetylgalactosamine‑6‑phosphate deacetylase |
| RA | 3,319,397 | G→C | 9.6% | P300A (CCG→GCG) | ftsH ← | protease, ATP‑dependent zinc‑metallo |
| RA | 3,332,937 | G→T | 6.8% | P163Q (CCG→CAG) | mlaF ← | ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein |
| RA | 3,365,687 | C→A | 8.7% | G83W (GGG→TGG) | nanT ← | sialic acid transporter |
| RA | 3,372,344 | G→A | 14.3% | P338L (CCG→CTG) | yhcM ← | putative AFG1‑like family P‑loop ATPase |
| RA | 3,401,370 | C→A | 6.1% | F135L (TTC→TTA) | panF → | pantothenate:sodium symporter |
| RA | 3,416,890 | T→G | 5.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,443,191 | A→G | 10.8% | W18R (TGG→CGG) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,457,678 | G→T | 7.1% | R133L (CGG→CTG) | gspL → | general secretory pathway component, cryptic |
| RA | 3,477,313 | C→T | 7.8% | D251D (GAC→GAT) | yheT → | UPF0017 family putative hydrolase |
| RA | 3,519,946 | C→A | 11.1% | A40E (GCG→GAG) | yrfF → | inner membrane protein |
| RA | 3,528,389 | A→G | 8.0% | I280T (ATC→ACC) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,615,780 | G→A | 8.2% | A1077T (GCC→ACC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,688,913 | C→A | 8.2% | pseudogene (433/753 nt) | bcsQ ← | involved in cellulose production, minD superfamily (pseudogene) |
| RA | 3,705,875 | C→A | 7.9% | V140V (GTG→GTT) | yhjY ← | autotransporter beta‑domain protein |
| RA | 3,782,065 | G→T | 6.8% | G202V (GGT→GTT) | yibQ → | putative polysaccharide deacetylase |
| RA | 3,785,553 | T→C | 7.7% | E120G (GAA→GGA) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,785,736 | G→T | 10.3% | P59H (CCT→CAT) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,824,963 | C→A | 7.4% | Q383K (CAA→AAA) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,900,875 | G→A | 11.4% | R22C (CGC→TGC) | phoU ← | negative regulator of PhoR/PhoB two‑component regulator |
| RA | 3,945,046 | C→T | 5.3% | pseudogene (145/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,983,733 | G→T | 9.1% | R132S (CGC→AGC) | hemC ← | hydroxymethylbilane synthase |
| RA | 3,988,643 | G→A | 10.0% | T174T (ACG→ACA) | dapF → | diaminopimelate epimerase |
| RA | 4,023,090 | G→T | 7.3% | T414T (ACC→ACA) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,075,650 | Δ1 bp | 7.0% | coding (470/903 nt) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,075,651 | Δ1 bp | 7.0% | coding (469/903 nt) | fdoH ← | formate dehydrogenase‑O, Fe‑S subunit |
| RA | 4,141,782 | G→T | 11.2% | I415I (ATC→ATA) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,165,449 | C→T | 30.9% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 31.0% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,178,209 | C→T | 13.2% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 100% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,196,529 | T→C | 10.5% | D311G (GAC→GGC) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,196,530 | C→G | 10.5% | D311H (GAC→CAC) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,196,532 | G→C | 10.5% | T310S (ACC→AGC) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,196,533 | T→G | 10.2% | T310P (ACC→CCC) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,196,534 | T→A | 10.3% | K309N (AAA→AAT) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,196,536 | T→G | 10.3% | K309Q (AAA→CAA) ‡ | purH ← | fused IMP cyclohydrolase/phosphoribosylaminoimidazolecarboxamide formyltransferase |
| RA | 4,221,518 | G→T | 10.3% | R14R (CGC→CGA) | yjbD ← | DUF3811 family protein |
| RA | 4,294,793 | G→A | 11.8% | S541F (TCC→TTC) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,334,762 | C→A | 6.4% | G205V (GGC→GTC) | yjdF ← | DUF2238 family inner membrane protein |
| RA | 4,417,684 | G→T | 11.8% | pseudogene (174/402 nt) | ytfA → | pseudogene, related to transcriptional regulators |
| RA | 4,432,615 | G→T | 6.7% | Q139H (CAG→CAT) | tamA → | translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,508,484 | C→T | 5.6% | A47A (GCC→GCT) | insA → | IS1 repressor TnpA |
| RA | 4,510,272 | C→A | 12.6% | intergenic (‑131/+216) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,544,594:1 | +C | 6.8% | coding (202/774 nt) | uxuR → | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor |
| RA | 4,544,598:1 | +G | 7.7% | coding (206/774 nt) | uxuR → | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor |
| RA | 4,548,736 | C→T | 16.4% | G203D (GGC→GAC) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,593,789 | G→T | 7.2% | G166C (GGT→TGT) | yjjQ → | putative transcriptional regulator |
| RA | 4,614,950 | C→A | 8.5% | A80E (GCA→GAA) | serB → | 3‑phosphoserine phosphatase |
| RA | 4,625,525 | G→T | 15.5% | G63V (GGT→GTT) | creA → | putative periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 80533 | 80629 | 97 | 4 [3] | [2] 4 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | CP009273 | 578971 | 579310 | 340 | 4 [3] | [3] 5 | [appY] | [appY] |
| * | * | ÷ | CP009273 | 2027301 | 2027459 | 159 | 4 [2] | [3] 6 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2622956 | 2623037 | 82 | 5 [3] | [3] 4 | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| * | * | ÷ | CP009273 | 3262621 | 3262716 | 96 | 4 [3] | [3] 5 | yhaC | pentapetide repeats‑related protein |
| * | * | ÷ | CP009273 | 3406946 | 3406981 | 36 | 5 [3] | [0] 4 | acrS/acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| * | * | ÷ | CP009273 | 3432081 | 3432489 | 409 | 7 [3] | [2] 4 | zntR | zntA gene transcriptional activator |
| * | * | ÷ | CP009273 | 3448777 | 3448837 | 61 | 4 [3] | [1] 4 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3798342 | 3798523 | 182 | 4 [1] | [3] 4 | [waaS]–[waaP] | [waaS],[waaP] |
| * | * | ÷ | CP009273 | 4037417 | 4037473 | 57 | 4 [2] | [3] 5 | dsbA/yihF | periplasmic protein disulfide isomerase I/DUF945 family protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 287112 | NA (NA) | 16 (0.460) | 9/248 | NT | 72.9% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | CP009273 | 1972854 = | 6 (0.170) | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 353194 | 31 (1.170) | 3 (0.120) | 3/186 | NT | 9.0% | intergenic (+29/+308) | codA/cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| ? | CP009273 | 1546506 = | NA (NA) | noncoding (1/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | 360104 = | 51 (1.450) | 21 (0.600) | 12/250 | NT | 29.2% | 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 | 16 (0.630) | 11 (0.480) | 4/164 | NT | 43.3% | 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 | 1203246 = | 8 (0.230) | 13 (0.430) | 9/218 | NT | 65.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 7 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 6 (0.170) | 15 (0.490) | 9/218 | NT | 71.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 7 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1972861 | 8 (0.230) | 29 (0.830) | 20/250 | NT | 78.4% | intergenic (‑407/‑373) | 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 | |||||