mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 59,123 | IS150 (+) +3 bp | coding (3‑5/159 nt) | yabQ → | protein YabQ |
| RA | 85,520 | C→T | intergenic (‑9/‑110) | yabR ← / → ilvI | protein YabR/acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 92,790 | C→T | P460S (CCG→TCG) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 204,147 | C→T | A267V (GCC→GTC) | lpxB → | lipid A disaccharide synthase |
| JC JC | 214,173 | IS2 (–) +5 bp | intergenic (‑48/‑114) | yaeP ← / → yaeQ | PF06786 family protein YaeP/uncharacterized protein YaeQ |
| RA | 229,802 | G→A | M212I (ATG→ATA) | dkgB → | methylglyoxal reductase DkgB |
| RA | 230,017 | G→A | L289F (CTT→TTT) | yafC ← | DNA‑binding transcriptional regulator YafC |
| RA | 238,884 | G→A | intergenic (‑148/+535) | ykfM ← / ← yafV | uncharacterized protein YkfM/2‑oxoglutaramate amidase |
| RA | 239,930 | G→A | S87F (TCT→TTT) | yafV ← | 2‑oxoglutaramate amidase |
| RA | 243,084 | G→A | R74C (CGC→TGC) | fadE ← | acyl‑CoA dehydrogenase |
| RA | 245,766 | G→A | P14S (CCG→TCG) | dpaA ← | peptidoglycan meso‑diaminopimelic acid protein amidase A |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| RA | 251,604 | G→A | S236N (AGC→AAC) | dinB → | DNA polymerase IV |
| RA | 252,349 | G→A | E17K (GAA→AAA) | yafO → | ribosome‑dependent mRNA interferase toxin YafO |
| RA | 253,835 | G→A | intergenic (+674/+424) | yafP → / ← pepD | putative N‑acetyltransferase YafP/peptidase D |
| RA | 266,523 | G→A | L11L (CTG→TTG) | yafY ← | inner membrane lipoprotein YafY |
| RA | 267,149 | G→A | intergenic (‑596/+35) | yafY ← / ← yafZ | inner membrane lipoprotein YafY/DUF932 domain‑containing protein YafZ |
| RA | 268,709 | G→A | R84R (CGC→CGT) | ykfA ← | putative GTP‑binding protein YkfA |
| RA | 273,450 | G→A | A202T (GCG→ACG) | ykfC → | PF00078 domain‑containing protein YkfC |
| RA | 273,734 | G→A | Q296Q (CAG→CAA) | ykfC → | PF00078 domain‑containing protein YkfC |
| RA | 274,939 | G→A | A48V (GCT→GTT) | insH1 ← | IS5 family transposase and trans‑activator |
| RA | 274,985 | G→A | P33S (CCA→TCA) | insH1 ← | IS5 family transposase and trans‑activator |
| RA | 275,668 | G→A | G115E (GGA→GAA) | mmuP → | S‑methyl‑L‑methionine transporter |
| RA | 277,277 | G→A | R188H (CGT→CAT) | mmuM → | homocysteine S‑methyltransferase |
| RA | 281,053 | T→C | T311A (ACG→GCG) | yagA ← | integrase core domain‑containing protein YagA |
| RA | 281,778 | G→A | S69F (TCC→TTC) | yagA ← | integrase core domain‑containing protein YagA |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 285,966 | G→A | G191D (GGC→GAC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 287,324 | G→A | G179D (GGC→GAC) | yagH → | putative xylosidase/arabinosidase |
| RA | 287,348 | G→A | G187D (GGC→GAC) | yagH → | putative xylosidase/arabinosidase |
| RA | 287,946 | G→A | W386* (TGG→TGA) | yagH → | putative xylosidase/arabinosidase |
| RA | 288,641 | G→A | A174A (GCC→GCT) | xynR ← | DNA‑binding transcriptional repressor XynR |
| RA | 294,857 | G→A | intergenic (‑58/+61) | yagM ← / ← ykgV | protein YagM/protein YkgV |
| RA | 295,209 | G→A | T124I (ACT→ATT) | yagN ← | protein YagN |
| RA | 298,897 | G→A | P680S (CCC→TCC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 305,439 | G→A | S460F (TCC→TTC) | ecpD ← | fimbrial adhesin EcpD |
| RA | 305,990 | G→A | I276I (ATC→ATT) | ecpD ← | fimbrial adhesin EcpD |
| RA | 308,924 | G→A | R137C (CGC→TGC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 310,789 | G→A | A183V (GCT→GTT) | matA ← | DNA‑binding transcriptional dual regulator MatA |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 314,622 | G→A | intergenic (‑1380/‑669) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 316,519 | G→A | intergenic (+66/+1207) | insF1 → / ← rclC | IS3 element protein InsF/DUF417 domain‑containing inner membrane protein RclC |
| RA | 316,837 | G→A | intergenic (+384/+889) | insF1 → / ← rclC | IS3 element protein InsF/DUF417 domain‑containing inner membrane protein RclC |
| RA | 320,300 | G→A | S25N (AGT→AAT) | rclR → | DNA‑binding transcriptional activator RclR |
| RA | 324,926 | G→A | P147S (CCT→TCT) | ykgH ← | uncharacterized protein YkgH |
| RA | 328,598 | C→T | V46I (GTC→ATC) | betB ← | betaine aldehyde dehydrogenase |
| RA | 339,376 | G→A | G351E (GGG→GAG) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 339,935 | C→T | A56V (GCC→GTC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,941 | C→T | T58I (ACT→ATT) | yahH → | putative uncharacterized protein YahH |
| RA | 339,958 | G→A | D64N (GAC→AAC) | yahH → | putative uncharacterized protein YahH |
| RA | 343,442 | G→A | G187R (GGA→AGA) | yahK → | aldehyde reductase, NADPH‑dependent |
| RA | 343,667 | G→A | G262S (GGC→AGC) | yahK → | aldehyde reductase, NADPH‑dependent |
| RA | 347,833 | G→A | A204V (GCC→GTC) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 352,642 | G→A | E476E (GAG→GAA) | prpD → | 2‑methylcitrate dehydratase |
| RA | 352,850 | G→A | G49S (GGC→AGC) | prpE → | propionyl‑CoA synthetase |
| RA | 353,100 | G→A | G132D (GGC→GAC) | prpE → | propionyl‑CoA synthetase |
| RA | 355,006 | G→A | G29R (GGA→AGA) | codB → | cytosine transporter |
| RA | 355,064 | G→A | S48N (AGC→AAC) | codB → | cytosine transporter |
| RA | 355,229 | G→A | G103E (GGA→GAA) | codB → | cytosine transporter |
| RA | 356,687 | G→A | A173T (GCG→ACG) | codA → | cytosine/isoguanine deaminase |
| RA | 357,285 | G→A | G372E (GGA→GAA) | codA → | cytosine/isoguanine deaminase |
| RA | 358,368 | G→A | P108L (CCC→CTC) | cynR ← | DNA‑binding transcriptional dual regulator CynR |
| RA | 360,082 | G→A | G31R (GGA→AGA) | cynX → | cyanate transporter |
| RA | 360,137 | G→A | G49D (GGC→GAC) | cynX → | cyanate transporter |
| RA | 360,536 | C→T | S182F (TCC→TTC) | cynX → | cyanate transporter |
| RA | 360,786 | G→A | M265I (ATG→ATA) | cynX → | cyanate transporter |
| RA | 361,489 | G→A | N124N (AAC→AAT) | lacA ← | galactoside O‑acetyltransferase |
| RA | 364,433 | G→A | Q625* (CAG→TAG) | lacZ ← | beta‑galactosidase |
| RA | 365,146 | G→A | A387V (GCC→GTC) | lacZ ← | beta‑galactosidase |
| RA | 365,222 | G→A | P362S (CCT→TCT) | lacZ ← | beta‑galactosidase |
| RA | 365,959 | G→A | P116L (CCC→CTC) | lacZ ← | beta‑galactosidase |
| RA | 366,121 | G→A | A62V (GCC→GTC) | lacZ ← | beta‑galactosidase |
| RA | 369,838 | G→A | A410T (GCG→ACG) | mhpA → | 3‑(3‑hydroxyphenyl)propanoate hydroxylase |
| RA | 371,869 | G→A | E211K (GAA→AAA) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 372,529 | G→A | V139M (GTG→ATG) | mhpD → | 2‑hydroxypentadienoate hydratase |
| RA | 373,341 | G→A | A141T (GCG→ACG) | mhpF → | acetaldehyde dehydrogenase (acetylating) MhpF |
| RA | 373,985 | C→T | R40C (CGC→TGC) | mhpE → | 4‑hydroxy‑2‑oxovalerate aldolase |
| RA | 374,227 | C→T | A120A (GCC→GCT) | mhpE → | 4‑hydroxy‑2‑oxovalerate aldolase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 382,571 | G→A | E300K (GAA→AAA) | insD1 → | IS2 element protein |
| RA | 382,943 | G→A | C331C (TGC→TGT) | yaiP ← | putative glucosyltransferase |
| RA | 384,839 | G→A | intergenic (‑223/‑393) | yaiS ← / → tauA | putative deacetylase YaiS/taurine ABC transporter periplasmic binding protein |
| RA | 385,382 | G→A | A51T (GCA→ACA) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 386,290 | G→A | E28E (GAG→GAA) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 387,624 | G→A | E218E (GAG→GAA) | tauC → | taurine ABC transporter membrane subunit |
| RA | 398,073 | G→A | G68R (GGG→AGG) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 398,494 | G→A | G208D (GGC→GAC) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 400,495 | G→A | V143V (GTC→GTT) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 403,108 | G→A | L454L (CTG→CTA) | phoA → | alkaline phosphatase |
| RA | 409,770 | G→A | L84L (CTG→TTG) | rdgC ← | nucleoid‑associated protein RdgC |
| RA | 413,029 | G→A | H909Y (CAT→TAT) | sbcC ← | ATP‑dependent structure‑specific DNA nuclease ‑ SbcC subunit |
| RA | 431,516 | A→C | Y166* (TAT→TAG) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 456,227 | G→A | E365E (GAG→GAA) | tig → | trigger factor |
| RA | 462,281 | G→A | A123T (GCG→ACG) | ppiD → | periplasmic folding chaperone |
| RA | 466,958 | C→T | D119N (GAT→AAT) | ybaE ← | uncharacterized protein YbaE |
| RA | 469,111 | C→T | L81L (CTG→TTG) | mdlA → | ABC transporter family protein MdlA |
| RA | 479,319 | G→A | intergenic (‑68/+48) | ylaC ← / ← maa | putative inner membrane protein/maltose O‑acetyltransferase |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| JC JC | 480,334 | IS5 (+) +4 bp | coding (372‑375/375 nt) | tomB ← | Hha toxicity modulator TomB |
| RA | 481,984 | G→A | S807F (TCT→TTT) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 481,990 | G→A | S805F (TCC→TTC) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 490,181 | G→A | L31L (CTG→TTG) | ybaM ← | DUF2496 domain‑containing protein YbaM |
| RA | 498,400 | G→A | A116T (GCA→ACA) | hemH → | ferrochelatase |
| RA | 501,781 | G→A | I486I (ATC→ATT) | ybaL ← | putative transporter YbaL |
| RA | 515,925 | G→A | E3K (GAA→AAA) | fetA → | putative iron ABC exporter ATP‑binding subunit FetA |
| RA | 524,376 | G→A | V372V (GTG→GTA) | rhsD → | protein RhsD |
| RA | 527,575 | G→A | intergenic (+34/‑6) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 528,092 | G→A | intergenic (+143/+1553) | ybbC → / ← ylbG | PF15631 family protein YbbC/putative DNA‑binding transcriptional regulator YlbG |
| RA | 528,534 | G→A | intergenic (+585/+1111) | ybbC → / ← ylbG | PF15631 family protein YbbC/putative DNA‑binding transcriptional regulator YlbG |
| RA | 531,590 | G→A | A211V (GCC→GTC) | allS ← | DNA‑binding transcriptional activator AllS |
| JC JC | 552,785 | IS150 (+) +3 bp | coding (314‑316/510 nt) | purE ← | N(5)‑carboxyaminoimidazole ribonucleotide mutase |
| RA | 558,686 | G→A | G159S (GGC→AGC) | sfmA → | putative fimbrial protein SfmA |
| RA | 559,732 | G→A | R12R (AGG→AGA) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 567,992 | G→A | K285K (AAG→AAA) | insF3 → | IS3 element protein InsF |
| RA | 570,416 | G→A | E505E (GAG→GAA) | ybcK → | putative recombinase YbcK |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| RA | 639,702 | G→A | intergenic (+194/‑51) | ahpC → / → ahpF | alkyl hydroperoxide reductase, AhpC component/alkyl hydroperoxide reductase, AhpF component |
| RA | 640,502 | C→A | L250L (CTC→CTA) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
| RA | 662,602 | G→A | P14L (CCT→CTT) | ybeD ← | DUF493 domain‑containing protein YbeD |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 692,073 | C→T | R90H (CGT→CAT) | ybeY ← | endoribonuclease YbeY |
| MC JC | 696,507 | Δ112 bp | glnV | glnV | |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 731,964 | G→A | W794* (TGG→TGA) | rhsC → | rhs element protein RhsC |
| RA | 738,681 | G→A | G197E (GGA→GAA) | ybfD → | H repeat‑associated putative transposase YbfD |
| RA | 742,600 | G→A | intergenic (‑44/‑227) | dtpD ← / → ybgI | dipeptide:H(+) symporter DtpD/radiation resistance protein YbgI |
| RA | 744,664 | G→A | G141D (GGC→GAC) | pxpC → | 5‑oxoprolinase component C |
| RA | 790,831 | G→A | P67S (CCC→TCC) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 806,806 | G→A | P159L (CCT→CTT) | ybhC ← | outer membrane lipoprotein YbhC |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 812,537 | G→A | E90K (GAG→AAG) | bioD → | dethiobiotin synthetase |
| RA | 866,125 | G→A | S80S (TCC→TCT) | moeA ← | molybdopterin molybdotransferase |
| RA | 896,829 | G→A | V232V (GTG→GTA) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 908,422 | G→A | G291G (GGC→GGT) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 946,493 | G→A | G208D (GGC→GAC) | ycaD → | putative transporter YcaD |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 974,621 | C→T | Y101Y (TAC→TAT) | mukF → | chromosome partitioning protein MukF |
| RA | 1,018,193 | C→T | S36N (AGT→AAT) | ycbZ ← | putative ATP‑dependent protease YcbZ |
| RA | 1,022,002 | C→T | E628K (GAG→AAG) | yccS ← | putative transporter YccS |
| RA | 1,023,148 | C→T | D246N (GAT→AAT) | yccS ← | putative transporter YccS |
| RA | 1,035,862 | C→T | A31A (GCC→GCT) | hyaD → | putative hydrogenase 1 maturation protease HyaD |
| RA | 1,036,085 | C→T | L106L (CTG→TTG) | hyaD → | putative hydrogenase 1 maturation protease HyaD |
| RA | 1,037,810 | C→T | P24L (CCC→CTC) | appC → | cytochrome bd‑II subunit 1 |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,043,376 | C→T | V279M (GTG→ATG) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,048,985 | C→T | L116L (CTG→CTA) | gfcB ← | lipoprotein GfcB |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,070,014 | A→G | L114P (CTG→CCG) | rutF ← | FMN reductase RutF |
| RA | 1,078,641 | A→C | F81C (TTT→TGT) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| MC JC | 1,095,503 | Δ10,045 bp | IS3‑mediated | ycdU–[ymdA] | ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, [ymdA] |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| JC JC | 1,141,668 | IS150 (+) +3 bp | coding (2698‑2700/3186 nt) | rne ← | ribonuclease E |
| JC JC | 1,145,135 | IS3 (+) +3 bp | coding (196‑198/960 nt) | rluC → | 23S rRNA pseudouridine(955/2504/2580) synthase |
| RA | 1,150,616 | C→T | L297L (CTG→TTG) | fabD → | [acyl‑carrier‑protein] S‑malonyltransferase |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| JC JC | 1,232,148 | IS2 (–) +5 bp | coding (963‑967/1269 nt) | umuC → | DNA polymerase V catalytic protein |
| RA | 1,265,552 | G→A | G181S (GGT→AGT) | prfA → | peptide chain release factor RF1 |
| RA | 1,276,230 | C→T | P463P (CCG→CCA) | narX ← | sensor histidine kinase NarX |
| JC JC | 1,301,713 | IS30 (–) +2 bp | coding (532‑533/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,315,384 | G→A | Y129Y (TAC→TAT) | yciF ← | DUF892 domain‑containing protein YciF |
| RA | 1,317,129 | G→A | Q32* (CAG→TAG) | trpA ← | tryptophan synthase subunit alpha |
| RA | 1,322,325 | G→A | L208F (CTC→TTC) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,356,932 | G→A | T60I (ACC→ATC) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,362,062 | C→A | T51K (ACG→AAG) | puuR → | DNA‑binding transcriptional repressor PuuR |
| RA | 1,366,433 | G→A | G295D (GGC→GAC) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| RA | 1,388,411 | G→A | A134V (GCC→GTC) | tpx ← | lipid hydroperoxide peroxidase |
| MC JC | 1,397,239 | Δ7,448 bp | IS5‑mediated | ynaJ–abgA | ynaJ, uspE, fnr, ogt, abgT, abgB, abgA |
| RA | 1,464,645 | C→T | Q59* (CAG→TAG) | paaY → | 2‑hydroxycyclohepta‑1,4,6‑triene‑1‑carboxyl‑CoA thioesterase |
| JC JC | 1,477,100 | IS5 (+) +4 bp | coding (1957‑1960/2307 nt) | ydbD → | DUF2773 domain‑containing protein YdbD |
| RA | 1,501,192 | C→T | P207L (CCT→CTT) | tehA → | tellurite resistance protein |
| RA | 1,510,574 | G→A | G191D (GGC→GAC) | ydcR → | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR |
| RA | 1,542,527 | G→A | H22Y (CAC→TAC) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,582,610 | G→T | intergenic (‑86/+316) | ydeN ← / ← ydeO | putative sulfatase YdeN/DNA‑binding transcriptional dual regulator YdeO |
| JC JC | 1,590,147 | IS2 (+) +5 bp | intergenic (‑146/+703) | ydeT ← / ← hipA | fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA |
| RA | 1,610,076 | T→G | D202A (GAT→GCT) | uxaB ← | tagaturonate reductase |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,688,866 | G→A | Q97Q (CAG→CAA) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| JC JC | 1,772,062 | IS5 (+) +4 bp | coding (992‑995/1215 nt) | ydiM → | putative exporter YdiM |
| RA | 1,774,952 | G→A | E89E (GAG→GAA) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,815,136 | G→A | G424S (GGT→AGT) | katE → | catalase HPII |
| JC JC | 1,844,254 | IS150 (+) +3 bp | coding (616‑618/1041 nt) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| MC JC | 1,867,696 | Δ7 bp | coding (789‑795/1935 nt) | yeaG → | protein kinase YeaG |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,907,451 | IS2 (+) +5 bp | coding (137‑141/144 nt) | yobF ← | DUF2527 domain‑containing protein YobF |
| RA | 1,987,499 | C→A | intergenic (+71/+8) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,137,858 | G→A | intergenic (‑615/‑44) | wza ← / → yegH | outer membrane polysaccharide export protein Wza/inner membrane protein YegH |
| RA | 2,188,087 | T→C | T110A (ACG→GCG) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,195,035 | G→A | A246T (GCG→ACG) | metG → | methionine‑‑tRNA ligase |
| JC JC | 2,324,384 | IS150 (+) +3 bp | coding (276‑278/651 nt) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit beta |
| RA | 2,384,808 | C→T | K305K (AAG→AAA) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,410,419 | G→A | L312L (CTG→TTG) | yfbS ← | putative transporter YfbS |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,572,542 | G→A | P322S (CCG→TCG) | eutD ← | phosphate acetyltransferase EutD |
| RA | 2,582,490 | C→T | L96L (TTG→TTA) | ypfG ← | DUF1176 domain‑containing protein YpfG |
| RA | 2,623,776 | G→A | E245K (GAG→AAG) | ppk → | polyphosphate kinase |
| RA | 2,663,960 | C→T | G173G (GGC→GGT) | suhB → | Nus factor SuhB |
| RA | 2,687,305 | C→T | G35D (GGC→GAC) | glnB ← | nitrogen regulatory protein PII‑1 |
| RA | 2,730,889 | G→A | noncoding (269/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 2,731,014 | C→T | noncoding (144/1542 nt) | rrsG ← | 16S ribosomal RNA |
| JC JC | 2,739,490 | IS150 (+) +3 bp | coding (578‑580/1122 nt) | tyrA ← | fused chorismate mutase/prephenate dehydrogenase |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| RA | 2,837,025 | C→T | C134Y (TGC→TAC) | hypF ← | carbamoyl‑‑[HypE] ligase |
| RA | 2,848,669 | C→T | L191L (CTG→CTA) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 2,869,618 | C→T | E219E (GAG→GAA) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,884,038 | C→T | W34* (TGG→TAG) | casA ← | type I‑E CRISPR system Cascade subunit CasA |
| RA | 2,893,165 | C→T | P170L (CCT→CTT) | ygcN → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 2,899,607 | C→T | A223T (GCA→ACA) | ygcW ← | putative deoxygluconate dehydrogenase |
| RA | 2,905,688 | C→T | I44I (ATC→ATT) | yqcG → | cell envelope stress response protein YqcG |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,924,229 | C→T | noncoding (296/369 nt) | csrB ← | small regulatory RNA CsrB |
| RA | 2,926,292 | C→T | intergenic (+96/‑16) | queF → / → ppnN | 7‑cyano‑7‑deazaguanine reductase/nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,934,993 | C→T | R253R (CGC→CGT) | fucP → | L‑fucose:H(+) symporter |
| RA | 2,941,835 | G→A | Q245* (CAA→TAA) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,960,736 | C→T | A565T (GCT→ACT) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,961,475 | C→T | E318E (GAG→GAA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,964,404 | C→T | G251D (GGC→GAC) | thyA ← | thymidylate synthase |
| RA | 2,974,745 | C→T | G424S (GGC→AGC) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyltransferase/acyl‑acyl carrier protein synthetase |
| RA | 2,991,238 | G→T | intergenic (‑878/‑30) | yqeK ← / → ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| RA | 2,991,649 | G→A | A128T (GCA→ACA) | ygeG → | TPR repeat‑containing putative chaperone YgeG |
| JC JC | 3,013,819 | IS150 (+) +3 bp | coding (419‑421/1626 nt) | yqeB ← | XdhC‑CoxI family protein YqeB |
| RA | 3,026,438 | C→T | L225L (CTG→TTG) | guaD → | guanine deaminase |
| RA | 3,027,460 | C→T | P114S (CCT→TCT) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,046,047 | C→T | intergenic (‑146/+121) | ygfF ← / ← gcvP | putative oxidoreductase YgfF/glycine decarboxylase |
| RA | 3,048,621 | C→T | D141N (GAT→AAT) | gcvP ← | glycine decarboxylase |
| RA | 3,051,404 | C→T | G305D (GGC→GAC) | ubiI ← | 2‑octaprenylphenol 6‑hydroxylase |
| RA | 3,076,262 | C→T | E399K (GAA→AAA) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,076,704 | C→T | A251A (GCG→GCA) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,099,319 | C→T | D83N (GAT→AAT) | yggM ← | DUF1202 domain‑containing protein YggM |
| RA | 3,102,165 | C→T | V230I (GTA→ATA) | trmB ← | tRNA m(7)G46 methyltransferase |
| RA | 3,103,765 | G→A | P251P (CCG→CCA) | mutY → | adenine DNA glycosylase |
| RA | 3,104,919 | C→T | L163L (CTG→TTG) | mltC → | membrane‑bound lytic murein transglycosylase C |
| RA | 3,108,369 | C→T | D263N (GAC→AAC) | speC ← | constitutive ornithine decarboxylase |
| RA | 3,108,690 | C→T | V156I (GTA→ATA) | speC ← | constitutive ornithine decarboxylase |
| RA | 3,109,473 | A→G | intergenic (‑73/‑80) | yqgH ← / → yqgA | protein YqgH/DUF554 domain‑containing protein YqgA |
| RA | 3,110,945 | C→T | S61N (AGC→AAC) | yghD ← | putative type II secretion system M‑type protein YghD |
| RA | 3,111,094 | C→T | Q11Q (CAG→CAA) | yghD ← | putative type II secretion system M‑type protein YghD |
| RA | 3,112,577 | C→T | G158D (GGC→GAC) | yghF ← | putative type II secretion system C‑type protein YghF |
| RA | 3,113,320 | C→T | G53E (GGA→GAA) | yghG ← | lipoprotein YghG |
| RA | 3,114,408 | C→T | intergenic (‑56/+142) | pppA ← / ← yghJ | prepilin peptidase/putative lipoprotein YghJ |
| RA | 3,115,379 | C→T | G1245D (GGT→GAT) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,116,951 | C→T | G721E (GGA→GAA) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,124,703 | C→T | A253T (GCG→ACG) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| MC JC | 3,131,341 | Δ18,049 bp | IS5‑mediated | [yghQ]–[yqhA] | 19 genes [yghQ], yghR, yghS, yghT, pitB, gss, yghU, hybG, hybF, hybE, hybD, hybC, hybB, hybA, hybO, yghW, yqhI, gpr, [yqhA] |
| RA | 3,157,803 | G→A | A52T (GCG→ACG) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,163,470 | G→A | I4I (ATC→ATT) | plsC ← | 1‑acylglycerol‑3‑phosphate O‑acyltransferase PlsC |
| RA | 3,166,108 | G→A | intergenic (‑135/+3) | parC ← / ← ygiS | DNA topoisomerase IV subunit A/putative deoxycholate binding periplasmic protein |
| RA | 3,166,913 | G→A | A269V (GCG→GTG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,167,825 | G→A | intergenic (‑107/+26) | ygiS ← / ← mqsA | putative deoxycholate binding periplasmic protein/antitoxin of the MqsRA toxin‑antitoxin system/DNA‑binding transcriptional repressor MqsA |
| RA | 3,168,872 | G→A | R120R (CGC→CGT) | ygiV ← | DNA‑binding transcriptional repressor YgiV |
| RA | 3,180,826 | G→A | E136K (GAA→AAA) | ygiC → | putative acid‑‑amine ligase YgiC |
| RA | 3,190,080 | G→A | G67D (GGC→GAC) | yqiH → | putative fimbrial chaperone YqiH |
| RA | 3,212,352 | G→A | G416S (GGC→AGC) | dnaG → | DNA primase |
| RA | 3,215,625 | G→A | noncoding (28/76 nt) | ileX → | tRNA‑Ile |
| RA | 3,222,872 | G→A | W80* (TGG→TGA) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,278,700 | G→A | intergenic (‑35/‑214) | agaR ← / → kbaZ | DNA‑binding transcriptional repressor AgaR/putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone |
| RA | 3,280,814 | G→A | intergenic (+124/‑1162) | agaV → / → agaS | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component/putative galactosamine‑6‑phosphate deaminase/isomerase |
| RA | 3,284,611 | G→A | V148I (GTC→ATC) | agaB → | galactosamine‑specific PTS enzyme IIB component |
| RA | 3,294,210 | G→A | V271I (GTA→ATA) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,295,067 | G→A | M556I (ATG→ATA) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,295,290 | G→A | A631T (GCA→ACA) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,300,725 | G→A | P12S (CCG→TCG) | yhbS ← | putative N‑acetyltransferase YhbS |
| RA | 3,307,890 | G→A | A15V (GCC→GTC) | yrbN ← | uncharacterized protein YrbN |
| RA | 3,318,274 | G→A | noncoding (16/77 nt) | metY ← | tRNA‑Met |
| RA | 3,323,624 | G→A | S149S (AGC→AGT) | glmM ← | phosphoglucosamine mutase |
| RA | 3,327,196 | G→A | P157S (CCA→TCA) | rlmE ← | 23S rRNA 2'‑O‑ribose U2552 methyltransferase |
| JC JC | 3,335,208 | IS150 (+) +4 bp | intergenic (+21/+24) | sfsB → / ← murA | putative transcriptional regulator SfsB/UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,336,411 | 2 bp→AT | coding (83‑84/1260 nt) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,347,801 | G→A | W229* (TGG→TGA) | rapZ → | RNase adaptor protein RapZ |
| RA | 3,348,518 | G→A | E23K (GAA→AAA) | yrbL → | protein kinase‑like domain‑containing protein YrbL |
| RA | 3,351,713 | G→A | S438F (TCT→TTT) | arcB ← | sensor histidine kinase ArcB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,429,229 | IS2 (+) +5 bp | intergenic (‑467/‑3) | rrsD ← / → yrdA | 16S ribosomal RNA/hexapeptide repeat‑containing protein YrdA |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,472,538 | G→A | T326I (ACC→ATC) | fusA ← | elongation factor G |
| RA | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| JC JC | 3,543,555 | IS150 (–) +3 bp | coding (389‑391/879 nt) | rpnA → | recombination‑promoting nuclease RpnA |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,575,597 | G→A | G176E (GGA→GAA) | yhgN → | MarC family putative inner membrane protein YhgN |
| RA | 3,609,228 | C→T | F4F (TTC→TTT) | yhhQ → | queuosine precursor transporter |
| RA | 3,628,866 | C→T | E225K (GAA→AAA) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,629,921 | C→T | E228K (GAG→AAG) | yhiI ← | putative membrane fusion protein YhiI |
| RA | 3,635,088 | G→A | G83E (GGG→GAG) | yhiM → | inner membrane protein YhiM |
| RA | 3,635,262 | G→A | S141N (AGC→AAC) | yhiM → | inner membrane protein YhiM |
| RA | 3,636,333 | G→A | P360S (CCT→TCT) | yhiN ← | putative oxidoreductase YhiN |
| RA | 3,639,029 | G→A | G463D (GGC→GAC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,649,205 | G→A | G91S (GGT→AGT) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,651,187 | G→A | intergenic (+525/‑104) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,656,809 | G→A | intergenic (‑69/‑186) | hdeA ← / → hdeD | periplasmic acid stress chaperone HdeA/acid‑resistance membrane protein |
| RA | 3,661,261 | G→A | G283D (GGC→GAC) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,662,374 | G→A | S654N (AGC→AAC) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,677,340 | G→A | I337I (ATC→ATT) | yhjG ← | AsmA family protein YhjG |
| RA | 3,682,101 | G→A | intergenic (‑161/+60) | yhjJ ← / ← dctA | peptidase M16 family protein YhjJ/C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,698,073 | G→A | L16L (CTG→CTA) | bcsF → | putative cellulose biosynthesis protein BcsF |
| RA | 3,702,034 | G→A | L279F (CTC→TTC) | dppF ← | dipeptide ABC transporter ATP binding subunit DppF |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,708,463 | 169 bp→A | [proK] | [proK] | |
| RA | 3,715,556 | G→A | S280F (TCT→TTT) | bisC ← | biotin sulfoxide reductase |
| RA | 3,716,798 | G→A | Q84Q (CAG→CAA) | yiaD → | PF13488 family lipoprotein YiaD |
| RA | 3,721,115 | G→A | D146N (GAT→AAT) | insJ → | insertion element IS150 protein InsA |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,731,831 | G→A | G234D (GGT→GAT) | xylF → | xylose ABC transporter periplasmic binding protein |
| RA | 3,748,288 | G→A | G402D (GGC→GAC) | lyxK → | L‑xylulose kinase |
| RA | 3,749,010 | G→A | G145E (GGG→GAG) | sgbH → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase SgbH |
| RA | 3,755,684 | G→A | I276I (ATC→ATT) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,759,817 | G→A | T15T (ACC→ACT) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,761,230 | G→A | S7F (TCC→TTC) | selA ← | selenocysteine synthase |
| RA | 3,761,858 | G→A | P33L (CCC→CTC) | yibF ← | glutathione transferase‑like protein YibF |
| RA | 3,764,316 | G→A | G712S (GGT→AGT) | rhsA → | rhs element protein RhsA |
| RA | 3,770,330 | G→A | Y350Y (TAC→TAT) | yibH ← | inner membrane protein YibH |
| RA | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,781,054 | G→A | intergenic (+37/‑161) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,781,861 | G→A | T234T (ACC→ACT) | cysE ← | serine acetyltransferase |
| RA | 3,793,266 | G→A | P140S (CCT→TCT) | htrL ← | protein HtrL |
| RA | 3,794,806 | G→A | A274T (GCG→ACG) | rfaD → | ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase |
| RA | 3,795,970 | G→A | A348T (GCC→ACC) | waaF → | ADP‑heptose‑‑LPS heptosyltransferase 2 |
| RA | 3,812,665 | G→A | intergenic (‑106/‑66) | yicR ← / → dfp | RadC‑like JAB domain‑containing protein YicR/fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,817,598 | G→A | intergenic (+59/‑162) | yicC → / → dinD | putative RNase adaptor protein YicC/DNA damage‑inducible protein D |
| RA | 3,819,317 | G→A | L148L (TTG→TTA) | yicG → | PF03458 family inner membrane protein YicG |
| JC | 3,822,651 | (CAGGAT)1→2 | coding (252/2109 nt) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,016 | G→T | R206L (CGC→CTC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,162 | C→T | H255Y (CAC→TAC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,854,009 | G→A | A30T (GCT→ACT) | emrD → | multidrug efflux pump EmrD |
| RA | 3,862,326 | G→A | Y49Y (TAC→TAT) | glvB ← | putative PTS enzyme II component GlvB |
| RA | 3,862,564 | G→A | A347V (GCC→GTC) | glvC ← | putative PTS enzyme II component GlvC |
| RA | 3,864,161 | G→A | G88E (GGA→GAA) | yidP → | putative DNA‑binding transcriptional regulator YidP |
| RA | 3,864,357 | G→A | L153L (CTG→CTA) | yidP → | putative DNA‑binding transcriptional regulator YidP |
| RA | 3,865,538 | G→A | P246S (CCT→TCT) | yidE ← | putative transport protein YidE |
| RA | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| RA | 3,871,022 | C→T | V237M (GTG→ATG) | dgoT ← | D‑galactonate:H(+) symporter |
| RA | 3,871,363 | G→A | P123L (CCG→CTG) | dgoT ← | D‑galactonate:H(+) symporter |
| RA | 3,872,298 | C→T | G234D (GGT→GAT) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,873,615 | G→A | A287V (GCT→GTT) | dgoK ← | 2‑dehydro‑3‑deoxygalactonokinase |
| RA | 3,873,698 | G→A | Y259Y (TAC→TAT) | dgoK ← | 2‑dehydro‑3‑deoxygalactonokinase |
| RA | 3,873,892 | G→A | L195F (CTT→TTT) | dgoK ← | 2‑dehydro‑3‑deoxygalactonokinase |
| RA | 3,875,237 | G→A | intergenic (‑77/‑201) | dgoR ← / → yidX | DNA‑binding transcriptional regulator DgoR/putative lipoprotein YidX |
| RA | 3,876,181 | C→T | D258N (GAT→AAT) | yidA ← | sugar phosphatase YidA |
| RA | 3,876,817 | G→A | P46S (CCG→TCG) | yidA ← | sugar phosphatase YidA |
| RA | 3,878,267 | G→A | A618V (GCT→GTT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,878,536 | G→A | Y528Y (TAC→TAT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,879,384 | C→T | E246K (GAA→AAA) | gyrB ← | DNA gyrase subunit B |
| RA | 3,883,804 | G→A | intergenic (‑75/‑222) | dnaA ← / → ysdD | chromosomal replication initiator protein DnaA/protein YsdD |
| RA | 3,883,818 | G→A | intergenic (‑89/‑208) | dnaA ← / → ysdD | chromosomal replication initiator protein DnaA/protein YsdD |
| RA | 3,893,459 | C→T | A232V (GCT→GTT) | yidZ → | DNA‑binding transcriptional dual regulator YidZ |
| RA | 3,894,943 | C→T | L98F (CTT→TTT) | yieF → | quinone reductase |
| RA | 3,896,736 | G→A | intergenic (‑127/‑38) | adeP ← / → yieH | adenine:H(+) symporter/6‑phosphogluconate phosphatase |
| RA | 3,898,481 | G→A | D154N (GAT→AAT) | cbrC → | PF03691 family colicin E2 tolerance protein CbrC |
| RA | 3,902,025 | G→A | R66C (CGT→TGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,909,205 | G→A | L79L (CTG→TTG) | pstA ← | phosphate ABC transporter membrane subunit PstA |
| RA | 3,912,074 | G→A | S532F (TCC→TTC) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,913,223 | G→A | A149V (GCT→GTT) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,915,731 | G→A | A81V (GCC→GTC) | atpC ← | ATP synthase F1 complex subunit epsilon |
| RA | 3,916,773 | G→A | D201D (GAC→GAT) | atpD ← | ATP synthase F1 complex subunit beta |
| RA | 3,917,983 | G→A | L95L (CTG→TTG) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,922,501 | G→A | intergenic (‑61/+556) | atpI ← / ← rsmG | ATP synthase accessory factor AtpI/16S rRNA m(7)G527 methyltransferase |
| RA | 3,923,432 | G→A | L83L (CTC→CTT) | rsmG ← | 16S rRNA m(7)G527 methyltransferase |
| RA | 3,924,585 | G→A | P350L (CCT→CTT) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,929,502 | G→A | V34V (GTC→GTT) | viaA ← | protein ViaA |
| RA | 3,931,952 | G→A | V213I (GTT→ATT) | kup → | K(+):H(+) symporter Kup |
| RA | 3,932,957 | G→A | V548I (GTA→ATA) | kup → | K(+):H(+) symporter Kup |
| RA | 3,933,173 | G→A | V620I (GTC→ATC) | kup → | K(+):H(+) symporter Kup |
| RA | 3,940,517 | G→A | T32T (ACC→ACT) | hsrA ← | putative transporter HsrA |
| RA | 3,941,924 | G→A | noncoding (117/1542 nt) | rrsC → | 16S ribosomal RNA |
| RA | 3,949,381 | C→T | E197K (GAA→AAA) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,959,263 | C→T | L432L (CTG→TTG) | ilvC → | ketol‑acid reductoisomerase (NADP(+)) |
| RA | 3,961,943 | G→A | E423K (GAG→AAG) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,963,162 | G→A | I356I (ATC→ATT) | gpp ← | guanosine‑5'‑triphosphate,3'‑diphosphate phosphatase |
| RA | 3,969,294 | G→A | M88I (ATG→ATA) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,972,573 | G→A | V18M (GTG→ATG) | rffG → | dTDP‑glucose 4,6‑dehydratase 2 |
| RA | 3,987,168 | C→T | A239T (GCG→ACG) | hemY ← | protein HemY |
| RA | 3,989,779 | C→T | S17N (AGC→AAC) | hemD ← | uroporphyrinogen‑III synthase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 3,996,049 | T→A | L156* (TTG→TAG) | yigA → | DUF484 domain‑containing protein YigA |
| RA | 4,011,802 | C→T | P243S (CCG→TCG) | bioP → | biotin transporter |
| RA | 4,029,054 | C→T | V640M (GTG→ATG) | fadB ← | multifunctional enoyl‑CoA hydratase, 3‑hydroxyacyl‑CoA epimerase, Delta(3)‑cis‑ Delta(2)‑trans‑enoyl‑CoA isomerase, L‑3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,032,682 | C→T | S64F (TCT→TTT) | yigZ → | IMPACT family member YigZ |
| RA | 4,037,229 | C→T | intergenic (+12/‑31) | ileT → / → alaT | tRNA‑Ile/tRNA‑Ala |
| RA | 4,084,903 | T→G | N307T (AAC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,092,703 | A→G | F41L (TTC→CTC) | frvA ← | putative PTS enzyme IIA component FrvA |
| RA | 4,093,564 | C→T | V237I (GTA→ATA) | rhaD ← | rhamnulose‑1‑phosphate aldolase |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,123,923 | +A | coding (534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,133,661 | C→T | intergenic (+155/‑174) | metF → / → katG | 5,10‑methylenetetrahydrofolate reductase/catalase/hydroperoxidase HPI |
| RA | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,161,248 | G→T | G61V (GGC→GTC) | fabR → | DNA‑binding transcriptional repressor FabR |
| RA | 4,164,123 | C→G | A162G (GCA→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,164,339 | G→A | W234* (TGG→TAG) | btuB → | cobalamin outer membrane transporter |
| RA | 4,164,868 | G→A | G410G (GGG→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,215,142 | G→A | W288* (TGG→TAG) | metA → | homoserine O‑succinyltransferase |
| RA | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,217,894 | C→T | F262F (TTC→TTT) | aceA → | isocitrate lyase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,282,332 | (A)5→6 | coding (744/1293 nt) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,313,171 | C→T | intergenic (‑180/‑179) | alsR ← / → rpiB | DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| JC JC | 4,365,462 | IS150 (–) +3 bp | intergenic (‑106/+8) | cutA ← / ← dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA |
| JC JC | 4,370,658 | IS150 (+) +3 bp | intergenic (‑246/‑28) | yjeH ← / → groS | L‑methionine/branched chain amino acid exporter/cochaperonin GroES |
| RA | 4,375,746 | G→A | M16I (ATG→ATA) | efp → | protein chain elongation factor EF‑P |
| RA | 4,384,822 | C→T | F328F (TTC→TTT) | yjeM → | putative transporter YjeM |
| JC JC | 4,385,870 | IS2 (–) +5 bp | coding (167‑171/315 nt) | yjeO → | DUF2645 domain‑containing inner membrane protein YjeO |
| RA | 4,389,397 | C→T | V322I (GTC→ATC) | psd ← | phosphatidylserine decarboxylase proenzyme |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,409,368 | G→A | E32K (GAA→AAA) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,414,939 | G→A | S222N (AGC→AAC) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,422,585 | G→A | V134I (GTT→ATT) | ulaD → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| JC JC | 4,430,711 | IS150 (–) +3 bp | coding (848‑850/1413 nt) | cycA → | D‑serine/alanine/glycine/:H(+)symporter |
| RA | 4,432,775 | G→A | S94S (TCC→TCT) | ytfF ← | inner membrane protein YtfF |
| RA | 4,443,596 | G→A | W405* (TGG→TGA) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,460,950 | C→T | G571S (GGT→AGT) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,465,585 | G→A | S199F (TCT→TTT) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,024 | C→T | P55S (CCG→TCG) | tabA → | DUF386 domain‑containing toxin‑antitoxin biofilm protein TabA |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,484,224 | G→A | S19S (AGC→AGT) | holC ← | DNA polymerase III subunit chi |
| RA | 4,488,217 | G→A | L300L (CTG→CTA) | lptG → | lipopolysaccharide transport system protein LptG |
| RA | 4,496,431 | A→G | noncoding (27/85 nt) | leuX → | tRNA‑Leu |
| RA | 4,496,440 | A→T | noncoding (36/85 nt) | leuX → | tRNA‑Leu |
| RA | 4,496,466 | G→A | noncoding (62/85 nt) | leuX → | tRNA‑Leu |
| RA | 4,499,501 | G→A | intergenic (+1/‑1759) | insD6 → / → yjgZ | IS2 insertion element protein InsB/uncharacterized protein YjgZ |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,512,541 | C→T | G290E (GGG→GAG) | fecC ← | ferric citrate ABC transporter membrane subunit FecC |
| RA | 4,512,767 | C→T | A215T (GCG→ACG) | fecC ← | ferric citrate ABC transporter membrane subunit FecC |
| RA | 4,518,043 | G→A | L65F (CTC→TTC) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,523,224 | G→A | L291F (CTC→TTC) | yjhG ← | D‑xylonate dehydratase |
| RA | 4,523,244 | C→T | G284D (GGC→GAC) | yjhG ← | D‑xylonate dehydratase |
| RA | 4,531,425 | C→T | R76H (CGC→CAC) | sgcX ← | putative endoglucanase with Zn‑dependent exopeptidase domain |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| RA | 4,536,716 | C→T | W293* (TGG→TGA) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| JC JC | 4,542,448 | IS5 (–) +4 bp | coding (412‑415/597 nt) | fimE → | regulator for fimA |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,553,339 | C→T | L147L (CTG→TTG) | uxuB → | D‑mannonate oxidoreductase |
| RA | 4,560,446 | C→T | G79S (GGC→AGC) | yjiH ← | uncharacterized protein YjiH |
| RA | 4,571,116 | C→T | E153E (GAG→GAA) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,577,627 | C→T | S111N (AGC→AAC) | mcrC ← | Type IV methyl‑directed restriction enzyme EcoKMcrBC subunit |
| RA | 4,578,534 | C→T | E268E (GAG→GAA) E268E (GAG→GAA) |
mcrB ← mcrB ← |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
| RA | 4,584,958 | C→T | A602T (GCC→ACC) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,589,433 | C→T | G616D (GGC→GAC) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,593,756 | C→T | G323R (GGG→AGG) | lgoT ← | galactonate:H(+) symporter |
| RA | 4,599,184 | C→T | G86G (GGG→GGA) | opgB ← | phosphoglycerol transferase I |
| RA | 4,605,340 | C→T | M108I (ATG→ATA) | fhuF ← | ferric‑siderophore reductase FhuF |
| RA | 4,609,336 | (C)7→8 | intergenic (+13/‑78) | yjjG → / → prfC | pyrimidine 5'‑nucleotidase YjjG/peptide chain release factor RF3 |
| RA | 4,622,949 | G→A | S394N (AGC→AAC) | yjjJ → | toxin YjjJ |
| RA | 4,623,854 | G→A | T88T (ACC→ACT) | lplA ← | lipoate‑‑protein ligase A |
| RA | 4,632,342 | C→T | S537F (TCT→TTT) | slt → | soluble lytic murein transglycosylase |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 257823 | 258675–257909 | 87–853 | 160 [0] | [0] 113 | crl–insA9 | crl,insB9,insA9 |
| * | * | ÷ | NC_000913 | 1196232 | 1211459 | 15228 | 43 [38] | [37] 39 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1492145 | 1492210 | 66 | 108 [0] | [0] 132 | [sokB] | [sokB] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 134 [0] | [0] 154 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2170353–2171427 | 2175000 | 3574–4648 | 39 [37] | [0] 86 | [insE5]–[gatA] | [insE5],insF5,gatR,gatD,gatB,[gatA] |
| * | * | ÷ | NC_000913 | 2755517 | 2755750 | 234 | 45 [35] | [37] 39 | [ssrA] | [ssrA] |
| * | * | ÷ | NC_000913 | 3223868 | 3262483 | 38616 | 102 [0] | [0] 108 | [ebgA]–[tdcD] | [ebgA],ebgC,ygjI,ygjJ,ygjK,fadH,higA,higB,rlmG,ygjP,ygjQ,ygjR,alx,sstT,ygjV,uxaA,uxaC,exuT,exuR,yqiM,yqjA,mzrA,yqjC,yqjD,yqjE,yqjK,yqjF,yqjG,yhaH,yhaI,yhaJ,yhaK,yhaL,cyuA,cyuP,tdcG,tdcF,tdcE,[tdcD] |
| * | * | ÷ | NC_000913 | 3423806–3424233 | 3424460–3424238 | 6–655 | 40 [38] | [38] 39 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257822 | 0 (0.000) | 158 (1.480) | 89/598 | 0.0 | 100% | intergenic (+51/‑7) | frsA/crl | fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 258676 = | 0 (0.000) | 77 (0.990) +81 bp |
50/436 | 0.2 | 100% | pseudogene (1/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | = 1469241 | NA (NA) | intergenic (‑92/‑5) | insC2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 144 (1.360) | 101/590 | 0.0 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 134 (1.250) | 91/598 | 0.0 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | = 1492144 | 0 (0.000) | 108 (1.020) | 69/592 | 0.2 | 100% | noncoding (26/57 nt) | sokB | putative small regulatory RNA antitoxin SokB |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 1492211 = | 0 (0.000) | 132 (1.240) | 79/594 | 0.1 | 100% | intergenic (+36/‑259) | sokB/trg | putative small regulatory RNA antitoxin SokB/methyl‑accepting chemotaxis protein Trg |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 154 (1.440) | 97/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | = 2170611 | NA (NA) | 86 (0.810) | 54/594 | 0.7 | 100% | noncoding (441/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 2175001 = | 0 (0.000) | coding (49/453 nt) | gatA | galactitol‑specific PTS enzyme IIA component | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 108 (1.010) | 65/596 | 0.3 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3262484 = | 0 (0.000) | coding (1177/1209 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_000913 | 3130146 = | NA (NA) | 102 (0.950) | 68/598 | 0.2 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3223867 | 0 (0.000) | coding (1235/3093 nt) | ebgA | evolved beta‑D‑galactosidase subunit alpha | |||||
| * | ? | NC_000913 | 4542682 = | 79 (0.740) | 67 (0.650) | 48/580 | 0.9 | 46.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 76 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 85 (0.790) | 52 (0.500) | 39/580 | 1.5 | 39.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 76 (0.730) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||