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 | 16,974 | IS150 (–) +3 bp | noncoding (23‑25/59 nt) | sokC → | small regulatory RNA antitoxin SokC |
| JC JC | 59,123 | IS150 (+) +3 bp | coding (3‑5/159 nt) | yabQ → | protein YabQ |
| RA | 92,790 | C→T | P460S (CCG→TCG) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| 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 |
| JC JC | 288,695 | IS150 (–) +3 bp | coding (466‑468/759 nt) | xynR ← | DNA‑binding transcriptional repressor XynR |
| 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 | 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 | 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 | 347,833 | G→A | A204V (GCC→GTC) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| 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 | 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 | 360,536 | 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 | 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 | 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 | 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 | 431,516 | A→C | Y166* (TAT→TAG) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| 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 |
| JC JC | 499,718 | IS150 (+) +3 bp | coding (254‑256/960 nt) | aes ← | acetylesterase |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| JC JC | 635,295 | IS150 (–) +3 bp | coding (80‑82/630 nt) | ybdM ← | ParB‑like nuclease domain‑containing protein YbdM |
| RA | 640,502 | C→A | L250L (CTC→CTA) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
| 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 | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| JC JC | 981,494 | IS150 (+) +4 bp | coding (448‑451/1848 nt) | ldtD → | L,D‑transpeptidase LdtD |
| JC JC | 989,526 | IS150 (–) +3 bp | coding (829‑831/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| 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 |
| 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 | 1,121,444 | IS150 (–) +4 bp | coding (41‑44/246 nt) | dinI ← | DNA damage‑inducible protein I |
| 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 |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| JC JC | 1,232,148 | IS2 (–) +5 bp | coding (963‑967/1269 nt) | umuC → | DNA polymerase V catalytic protein |
| 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 |
| JC JC | 1,383,055 | IS5 (–) +4 bp | coding (904‑907/999 nt) | ycjW ← | DNA‑binding transcriptional repressor YcjW |
| RA | 1,398,976 | C→T | R184H (CGC→CAC) | fnr ← | DNA‑binding transcriptional dual regulator FNR |
| RA | 1,400,978 | C→T | G266S (GGT→AGT) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| RA | 1,409,179 | C→T | noncoding (51/122 nt) | fnrS → | small regulatory RNA FnrS |
| MC JC | 1,411,925 | Δ23,060 bp | [ttcA]–ynaM | 34 genes [ttcA], intR, xisR, rcbA, ralA, ralR, recT, recE, racC, ydaE, kilR, kilS, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzoR, trkG, ynaK, ydaY, ynaA, lomR, insH5, lomR, stfR, tfaR, pinR, ynaE, ynaM |
|
| JC JC | 1,461,938 | IS150 (–) +4 bp | coding (1046‑1049/1206 nt) | paaJ → | beta‑ketoadipyl‑CoA thiolase |
| JC JC | 1,492,142 | IS150 (–) +3 bp | noncoding (24‑26/57 nt) | sokB → | putative small regulatory RNA antitoxin SokB |
| RA | 1,495,044 | G→A | R10C (CGC→TGC) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,501,192 | C→T | P207L (CCT→CTT) | tehA → | tellurite resistance protein |
| 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 | 1,701,306 | A→G | H117R (CAC→CGC) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| JC JC | 1,754,450 | IS5 (+) +4 bp | coding (25‑28/627 nt) | ydhY ← | putative 4Fe‑4S ferredoxin‑like protein YdhY |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| MC JC | 1,867,696 | Δ7 bp | coding (789‑795/1935 nt) | yeaG → | protein kinase YeaG |
| JC | 1,892,657 | (CAC)3→2 | coding (577‑579/1911 nt) | yoaA ← | putative ATP‑dependent 5' to 3' DNA helicase |
| 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 |
| JC JC | 2,020,326 | IS150 (+) +3 bp | coding (240‑242/1005 nt) | fliM → | flagellar motor switch protein FliM |
| JC JC | 2,024,681 | IS5 (–) +4 bp | coding (140‑143/189 nt) | dsrB ← | protein DsrB |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,043,522 | C→A | noncoding (36/90 nt) | serU ← | tRNA‑Ser |
| 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 |
| 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 |
| JC JC | 2,595,420 | IS150 (–) +3 bp | coding (438‑440/2016 nt) | tmcA ← | tRNA(Met) cytidine acetyltransferase |
| RA | 2,623,776 | G→A | E245K (GAG→AAG) | ppk → | polyphosphate kinase |
| RA | 2,730,889 | G→A | noncoding (269/1542 nt) | rrsG ← | 16S ribosomal RNA |
| JC JC | 2,739,490 | IS150 (+) +3 bp | coding (578‑580/1122 nt) | tyrA ← | fused chorismate mutase/prephenate dehydrogenase |
| JC JC | 2,757,363 | IS150 (–) +3 bp | coding (1205‑1207/1242 nt) | intA → | integrase IntA |
| RA | 2,777,982 | Δ1 bp | intergenic (+200/+164) | ypjF → / ← ypjA | toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,926,292 | C→T | intergenic (+96/‑16) | queF → / → ppnN | 7‑cyano‑7‑deazaguanine reductase/nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,941,835 | G→A | Q245* (CAA→TAA) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,991,238 | G→T | intergenic (‑878/‑30) | yqeK ← / → ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,103,765 | G→A | P251P (CCG→CCA) | mutY → | adenine DNA glycosylase |
| RA | 3,108,369 | C→T | D263N (GAC→AAC) | speC ← | constitutive ornithine decarboxylase |
| 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 | 3,113,320 | 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 | 3,124,703 | C→T | A253T (GCG→ACG) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | 3,145,112 | G→A | A10V (GCC→GTC) | hybA ← | hydrogenase 2 iron‑sulfur protein |
| 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 | 3,225,570 | G→A | V980M (GTG→ATG) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,228,771 | G→A | G324D (GGC→GAC) | ygjJ → | protein YgjJ |
| RA | 3,230,188 | G→A | W434* (TGG→TAG) | ygjK → | glycoside hydrolase |
| RA | 3,230,498 | G→A | L537L (TTG→TTA) | ygjK → | glycoside hydrolase |
| RA | 3,235,587 | G→A | L97F (CTC→TTC) | rlmG ← | 23S rRNA m(2)G1835 methyltransferase |
| RA | 3,241,603 | G→A | L48L (CTG→TTG) | ygjV ← | inner membrane protein |
| RA | 3,247,880 | G→A | L36L (TTG→TTA) | yqjA → | DedA family protein YqjA |
| RA | 3,252,424 | G→A | D41N (GAT→AAT) | yhaH → | putative inner membrane protein |
| RA | 3,257,443 | G→A | L190L (CTG→TTG) | cyuP ← | cysteine detoxification protein CyuP |
| JC JC | 3,262,484 | IS5 (+) +4 bp | coding (1174‑1177/1209 nt) | tdcD ← | propionate kinase |
| 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 |
| 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 |
| MC JC | 3,361,543 | Δ4,013 bp | IS5‑mediated | [gltF]–[yhcE] | [gltF], yhcA, yhcD, [yhcE] |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,609,228 | C→T | F4F (TTC→TTT) | yhhQ → | queuosine precursor transporter |
| JC JC | 3,611,865 | IS150 (–) +3 bp | coding (1‑3/1050 nt) | yhhT → | putative transporter YhhT |
| 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 | 3,662,374 | G→A | S654N (AGC→AAC) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| 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 | 3,708,467 | Δ168 bp | [proK] | [proK] | |
| 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 | 3,759,817 | 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 | 3,770,330 | 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 | 3,781,861 | G→A | T234T (ACC→ACT) | cysE ← | serine acetyltransferase |
| RA | 3,793,266 | G→A | P140S (CCT→TCT) | htrL ← | protein HtrL |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| 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 | 3,864,357 | G→A | L153L (CTG→CTA) | yidP → | putative DNA‑binding transcriptional regulator YidP |
| RA | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| RA | 3,871,363 | G→A | P123L (CCG→CTG) | dgoT ← | D‑galactonate:H(+) symporter |
| 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 | 3,876,817 | 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 | 3,883,818 | G→A | intergenic (‑89/‑208) | dnaA ← / → ysdD | chromosomal replication initiator protein DnaA/protein YsdD |
| 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 | 3,912,074 | 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 | 3,922,501 | G→A | intergenic (‑61/+556) | atpI ← / ← rsmG | ATP synthase accessory factor AtpI/16S rRNA m(7)G527 methyltransferase |
| RA | 3,933,173 | G→A | V620I (GTC→ATC) | kup → | K(+):H(+) symporter Kup |
| 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 | 3,989,779 | 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 | 4,032,682 | 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 |
| JC JC | 4,190,105 | IS2 (+) +5 bp | coding (320‑324/540 nt) | yjaZ → | protein YjaZ |
| 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 | 4,223,638 | 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 |
| 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 | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,499,661 | T→C | intergenic (+161/‑1599) | 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 | 4,523,244 | 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 | 4,632,342 | 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 | 258675–257908 | 86–853 | 128 [0] | [0] 72 | crl–insA9 | crl,insB9,insA9 |
| * | * | ÷ | NC_000913 | 1196299 | 1211429 | 15131 | 32 [31] | [31] 32 | [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 | 1263831 | 1264360 | 530 | 32 [31] | [31] 36 | hemA | glutamyl‑tRNA reductase |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 116 [0] | [0] 139 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2170367–2171427 | 2175000 | 3574–4634 | 33 [31] | [0] 74 | [insE5]–[gatA] | [insE5],insF5,gatR,gatD,gatB,[gatA] |
| * | * | ÷ | NC_000913 | 3423839–3424234 | 3424412–3424239 | 6–574 | 32 [29] | [31] 32 | [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) | 123 (1.310) | 84/598 | 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) | 51 (0.750) +81 bp |
34/436 | 0.7 | 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) | 102 (1.100) | 71/590 | 0.1 | 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) | 116 (1.240) | 80/598 | 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 | 1979271 = | 0 (0.000) | 138 (1.470) | 85/598 | 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) | 74 (0.800) | 51/594 | 0.5 | 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 | 4542682 = | 72 (0.770) | 81 (0.890) | 53/580 | 0.4 | 54.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 66 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 83 (0.890) | 71 (0.780) | 42/580 | 0.9 | 49.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 66 (0.730) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||