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 |
| RA | 3,645 | 2 bp→AT | coding (845‑846/933 nt) | thrB → | homoserine kinase |
| RA | 71,170 | T→C | S262P (TCG→CCG) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 81,102 | G→A | S286L (TCG→TTG) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 88,756 | C→T | F243F (TTC→TTT) | cra → | DNA‑binding transcriptional dual regulator Cra |
| RA | 98,060 | G→T | G325V (GGC→GTC) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase |
| RA | 108,958 | G→T | G227V (GGC→GTC) | secA → | protein translocation ATPase |
| RA | 154,182 | C→T | L415L (CTG→CTA) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 156,068 | A→G | V45A (GTA→GCA) | yadV ← | putative fimbrial chaperone YadV |
| RA | 169,496 | Δ1 bp | coding (2013/2244 nt) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 258,999 | Δ14,956 bp | IS5‑mediated | [crl]–[ykfC] | 21 genes [crl], phoE, proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| MC | 279,931 | Δ11,471 bp | between IS1 | yagB–insA3 | yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, argL, ykgS, insB3, insA3 |
| RA | 292,019 | C→T | L174L (CTA→TTA) | yagJ → | protein YagJ |
| RA | 309,381 | C→T | D216N (GAT→AAT) | ecpB ← | putative fimbrial chaperone EcpB |
| RA | 309,985 | T→A | G14G (GGA→GGT) | ecpB ← | putative fimbrial chaperone EcpB |
| RA | 319,825 | C→T | Q59Q (CAG→CAA) | rclA ← | cupric reductase RclA |
| RA | 339,048 | C→T | H242Y (CAT→TAT) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 351,263 | G→A | V17I (GTT→ATT) | prpD → | 2‑methylcitrate dehydratase |
| JC JC | 362,204 | IS1 (–) +9 bp | coding (968‑976/1254 nt) | lacY ← | lactose permease |
| RA | 380,909 | C→A | pseudogene (352/417 nt) | yaiX ← | putative acyltransferase, N‑terminal fragment |
| RA | 405,292 | G→T | A118D (GCC→GAC) | proC ← | pyrroline‑5‑carboxylate reductase |
| RA | 410,666 | C→T | P175S (CCT→TCT) | mak → | fructokinase |
| RA | 421,027 | C→T | R14R (CGC→CGT) | proY → | putative transporter ProY |
| JC JC | 431,304 | IS1 (–) +9 bp | coding (702‑710/885 nt) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 463,731 | G→A | S606N (AGT→AAT) | ppiD → | periplasmic folding chaperone |
| RA | 472,849 | A→G | G84G (GGA→GGG) | glnK → | nitrogen regulatory protein PII‑2 |
| RA | 495,622 | C→T | T168I (ACC→ATC) | htpG → | chaperone protein HtpG |
| RA | 534,742 | G→A | G276D (GGT→GAT) | gcl → | glyoxylate carboligase |
| RA | 539,897 | G→A | E251K (GAA→AAA) | allB → | allantoinase |
| RA | 552,850 | G→T | T84K (ACG→AAG) | purE ← | N(5)‑carboxyaminoimidazole ribonucleotide mutase |
| RA | 574,255 | G→A | Q100Q (CAG→CAA) | quuD → | prophage antitermination protein Q homolog QuuD |
| MC JC | 575,786 | Δ3,398 bp | IS5‑mediated | [nmpC]–borD | [nmpC], essD, rrrD, rzpD, rzoD, borD |
| RA | 582,277 | C→T | intergenic (+180/‑598) | tfaD → / → tfaX | putative tail fiber assembly protein TfaD/protein TfaX |
| RA | 582,597 | C→T | intergenic (+500/‑278) | tfaD → / → tfaX | putative tail fiber assembly protein TfaD/protein TfaX |
| RA | 620,757 | G→A | T144T (ACC→ACT) | fepG ← | ferric enterobactin ABC transporter membrane subunit FepG |
| RA | 634,877 | C→T | G167E (GGA→GAA) | ybdM ← | ParB‑like nuclease domain‑containing protein YbdM |
| RA | 635,281 | G→A | I32I (ATC→ATT) | ybdM ← | ParB‑like nuclease domain‑containing protein YbdM |
| RA | 650,062 | C→T | G143G (GGG→GGA) | citE ← | citrate lyase beta subunit |
| RA | 658,024 | G→T | intergenic (‑86/‑923) | crcB ← / → tatE | F(‑) channel protein/twin arginine protein translocation system ‑ TatE protein |
| RA | 662,857 | C→T | T369T (ACG→ACA) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase DacA |
| RA | 667,216 | G→T | P334P (CCC→CCA) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 681,755 | C→T | A547T (GCG→ACG) | hscC ← | chaperone protein HscC |
| RA | 694,941 | G→A | L5L (CTC→CTT) | miaB ← | isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 769,388 | A→T | I471F (ATC→TTC) | mngB → | alpha‑mannosidase |
| RA | 780,624 | C→T | noncoding (71/76 nt) | lysT → | tRNA‑Lys |
| RA | 789,580 | C→A | E134* (GAA→TAA) | galK ← | galactokinase |
| RA | 822,527 | C→T | E405K (GAA→AAA) | clsB ← | cardiolipin synthase B |
| RA | 855,793 | A→G | intergenic (‑49/‑170) | ldtB ← / → ybiT | L,D‑transpeptidase LdtB/putative ATP‑binding protein YbiT |
| RA | 883,396 | C→T | intergenic (‑8/‑277) | ybjG ← / → mdfA | undecaprenyl pyrophosphate phosphatase/multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 908,169 | C→T | R38R (AGG→AGA) | ybjT ← | putative NAD(P)‑binding protein YbjT |
| RA | 953,082 | A→G | L158P (CTG→CCG) | pflB ← | pyruvate formate‑lyase |
| RA | 980,038 | G→A | R1238H (CGC→CAC) | mukB → | chromosome partitioning protein MukB |
| MC JC | 1,076,135 | Δ80 bp | coding (2669‑2748/3963 nt) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,123,823 | 2 bp→AG | coding (231‑232/648 nt) | grxB ← | reduced glutaredoxin 2 |
| RA | 1,147,792 | T→A | S58T (TCG→ACG) | plsX → | putative phosphate acyltransferase |
| 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 | 1,194,922 | G→A | T10T (ACC→ACT) | rluE ← | 23S rRNA pseudouridine(2457) synthase |
| 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 | 1,253,002 | C→T | intergenic (+17/+83) | dhaR → / ← ycgV | DNA‑binding transcriptional dual regulator DhaR/putative autotransporter adhesin YcgV |
| JC JC | 1,290,524 | IS1 (–) +9 bp | coding (283‑291/1014 nt) | rssB → | regulator of RpoS |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 | 1,308,684 | T→C | intergenic (‑39/‑104) | clsA ← / → yciY | cardiolipin synthase A/uncharacterized protein YciY |
| RA | 1,322,532 | C→A | E139* (GAA→TAA) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,323,819 | G→A | G200G (GGG→GGA) | rnm → | RNase AM |
| RA | 1,329,565 | G→A | K78K (AAG→AAA) | sohB → | S49 peptidase family protein |
| RA | 1,331,059 | 2 bp→AT | coding (12‑13/2598 nt) | topA → | DNA topoisomerase 1 |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,349,872 | G→A | T79I (ACC→ATC) | yciW ← | putative peroxidase YciW |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,376,356 | G→A | R108H (CGC→CAC) | ycjR → | 3‑dehydro‑D‑guloside 4‑epimerase |
| RA | 1,381,277 | G→A | intergenic (+470/‑670) | ycjU → / → ompG | beta‑phosphoglucomutase/outer membrane porin G |
| RA | 1,381,637 | G→A | intergenic (+830/‑310) | ycjU → / → ompG | beta‑phosphoglucomutase/outer membrane porin G |
| RA | 1,397,837 | C→A | Q262H (CAG→CAT) | uspE ← | universal stress protein E |
| RA | 1,405,758 | G→A | intergenic (‑7/‑221) | mcaS ← / → smrA | small regulatory RNA McaS/DNA endonuclease SmrA |
| RA | 1,422,400 | G→A | V140I (GTT→ATT) | ydaV → | putative ATP‑binding protein YdaV |
| RA | 1,423,537 | G→A | W46* (TGG→TGA) | rzoR → | putative prophage outer membrane lipoprotein RzoR |
| RA | 1,426,810 | G→A | E119E (GAG→GAA) | ynaA → | putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,432,971 | G→A | W187* (TGG→TGA) | tfaR → | putative tail fiber assembly protein TfaR |
| RA | 1,435,877 | G→A | N339N (AAC→AAT) | ompN ← | outer membrane porin N |
| RA | 1,491,485 | G→A | noncoding (22/65 nt) | rydC ← | small regulatory RNA RydC |
| RA | 1,497,385 | 4 bp→CAA | coding (530‑533/1656 nt) | opgD → | glucans biosynthesis protein D |
| RA | 1,558,340 | G→A | S226S (AGC→AGT) | ddpD ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD |
| JC JC | 1,590,536 | IS2 (+) +5 bp | intergenic (‑535/+314) | ydeT ← / ← hipA | fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA |
| RA | 1,629,247 | C→T | I11I (ATC→ATT) | ydfZ → | putative selenoprotein YdfZ |
| RA | 1,638,244 | 2 bp→AG | coding (9‑10/66 nt) | ynfR ← | protein YnfR |
| 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 | 1,658,370 | C→T | S101F (TCC→TTC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,667,460 | G→A | Q369* (CAG→TAG) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,674,654 | C→A | P248T (CCT→ACT) | tqsA → | autoinducer 2 exporter |
| RA | 1,682,459 | A→G | K101E (AAA→GAA) | rstA → | DNA‑binding transcriptional regulator RstA |
| RA | 1,748,841 | C→T | R240K (AGA→AAA) | ydhT ← | uncharacterized protein YdhT |
| RA | 1,753,888 | G→C | A197G (GCG→GGG) | ydhY ← | putative 4Fe‑4S ferredoxin‑like protein YdhY |
| RA | 1,767,014 | C→T | G558S (GGT→AGT) | ydiJ ← | putative FAD‑linked oxidoreductase YdiJ |
| RA | 1,796,924 | G→A | L341L (CTG→TTG) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,814,677 | G→A | G271S (GGC→AGC) | katE → | catalase HPII |
| RA | 1,829,758 | G→A | R336R (CGC→CGT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,848,300 | 2 bp→TT | coding (376‑377/552 nt) | ydjA ← | putative oxidoreductase YdjA |
| RA | 1,849,629 | T→C | L265L (TTA→CTA) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,931,995 | A→G | E372G (GAG→GGG) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,041,278 | G→A | intergenic (+160/‑97) | msrQ → / → zinT | membrane‑bound flavocytochrome MsrQ/metal‑binding protein ZinT |
| RA | 2,052,885 | G→A | intergenic (+871/‑758) | yeeJ → / → shiA | inverse autotransporter adhesin/shikimate:H(+) symporter |
| RA | 2,095,666 | G→C | G181A (GGC→GCC) | hisA → | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino]imidazole‑4‑ carboxamide isomerase |
| RA | 2,095,818 | A→T | K232* (AAA→TAA) | hisA → | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino]imidazole‑4‑ carboxamide isomerase |
| RA | 2,104,024 | G→T | I162I (ATC→ATA) | wbbK ← | putative glycosyltransferase WbbK |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,142,598 | G→A | L117L (CTC→CTT) | udk ← | uridine/cytidine kinase |
| RA | 2,155,197 | G→A | Q394Q (CAG→CAA) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,176,844 | IS4 (–) +13 bp | coding (349‑361/855 nt) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,214,092 | C→G | V185L (GTC→CTC) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,233,609 | C→T | Q4* (CAG→TAG) | yeiS → | DUF2542 domain‑containing protein YeiS |
| JC JC | 2,238,948 | Δ1 bp :: IS186 (–) +6 bp :: Δ2 bp | coding (337‑342/1521 nt) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,242,247 | C→T | G241R (GGG→AGG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| RA | 2,247,134 | A→C | Y467D (TAC→GAC) | lysP ← | lysine:H(+) symporter |
| RA | 2,268,622 | T→A | V265E (GTG→GAG) | yeiR → | zinc‑binding GTPase YeiR |
| RA | 2,270,181 | C→A | S68* (TCG→TAG) | mepS → | peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| RA | 2,270,384 | C→T | L136L (CTG→TTG) | mepS → | peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| RA | 2,292,114 | C→T | P99P (CCG→CCA) | ccmH ← | holocytochrome c synthase CcmH component |
| RA | 2,307,733 | C→T | A295T (GCG→ACG) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,310,878 | 2 bp→TT | coding (656‑657/1056 nt) | ftp ← | FAD:protein FMN transferase |
| RA | 2,323,636 | C→T | L64F (CTC→TTC) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| RA | 2,404,402 | G→A | S71L (TCG→TTG) | nuoB ← | NADH:quinone oxidoreductase subunit B |
| RA | 2,446,592 | C→A | P294P (CCG→CCT) | aroC ← | chorismate synthase |
| RA | 2,455,977 | G→A | intergenic (‑331/+350) | yfcV ← / ← sixA | putative fimbrial protein YfcV/phosphohistidine phosphatase SixA |
| RA | 2,468,250 | G→A | E13K (GAA→AAA) | yfdH → | bactoprenol glucosyl transferase |
| RA | 2,483,558 | G→A | intergenic (‑219/‑171) | emrK ← / → evgL | tripartite efflux pump membrane fusion protein EmrK/protein EvgL |
| RA | 2,485,636 | Δ1 bp | coding (1263/3594 nt) | evgS → | sensor histidine kinase EvgS |
| RA | 2,485,638 | T→A | L422* (TTA→TAA) | evgS → | sensor histidine kinase EvgS |
| RA | 2,522,369 | G→A | P37S (CCG→TCG) | xapR ← | DNA‑binding transcriptional activator XapR |
| RA | 2,535,775 | A→C | E570D (GAA→GAC) | ptsI → | PTS enzyme I |
| RA | 2,558,170 | C→T | V170V (GTG→GTA) | eutB ← | ethanolamine ammonia‑lyase subunit alpha |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,637,757 | A→C | V299G (GTC→GGC) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,693,388 | G→A | A719V (GCG→GTG) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,702,085 | G→A | P129S (CCC→TCC) | recO ← | recombination mediator protein RecO |
| RA | 2,702,363 | G→A | A36V (GCC→GTC) | recO ← | recombination mediator protein RecO |
| RA | 2,703,619 | G→A | P149S (CCA→TCA) | rnc ← | RNase III |
| RA | 2,707,495 | C→T | D103N (GAC→AAC) | rseC ← | protein RseC |
| RA | 2,709,220 | G→A | A62V (GCC→GTC) | rseA ← | anti‑sigma‑E factor RseA |
| RA | 2,737,133 | G→A | intergenic (+250/‑21) | bamD → / → raiA | outer membrane protein assembly factor BamD/ribosome‑associated inhibitor A |
| RA | 2,737,590 | G→A | intergenic (+48/‑9) | raiZ → / → pheL | small RNA RaiZ/phe operon leader peptide |
| RA | 2,748,741 | G→A | Q260Q (CAG→CAA) | ypjD → | cytochrome c assembly family protein |
| RA | 2,769,594 | G→A | intergenic (+108/‑109) | yfjQ → / → yfjR | DUF932 domain‑containing protein YfjQ/putative DNA‑binding transcriptional regulator YfjR |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| RA | 2,803,859 | G→A | A120T (GCC→ACC) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,810,385 | G→A | V14V (GTG→GTA) | ygaH → | L‑valine exporter, YgaH component |
| RA | 2,818,668 | G→A | intergenic (‑23/+293) | serV ← / ← csrA | tRNA‑Ser/carbon storage regulator |
| RA | 2,826,108 | G→A | E93K (GAA→AAA) | srlA → | sorbitol‑specific PTS enzyme IIC2 component |
| RA | 2,838,419 | G→A | P282P (CCC→CCT) | ascG ← | DNA‑binding transcriptional repressor AscG |
| RA | 2,856,383 | G→A | K682K (AAG→AAA) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | 2,857,187 | G→A | R32Q (CGG→CAG) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,311 | G→T | R81S (CGT→AGT) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,880,635 | T→C | L138L (TTA→TTG) | casD ← | type I‑E CRISPR system Cascade subunit CasD |
| RA | 2,892,535 | G→A | V108I (GTA→ATA) | queD → | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,894,076 | G→A | S53N (AGT→AAT) | ygcO → | putative 4Fe‑4S cluster‑containing protein |
| RA | 2,902,376 | G→A | A161T (GCT→ACT) | ygcE → | putative sugar kinase YgcE |
| RA | 2,906,563 | G→A | G285S (GGC→AGC) | ygcG → | TPM domain‑containing protein YgcG |
| RA | 2,906,909 | G→A | Q345* (CAG→TAG) | eno ← | enolase |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,928,947 | G→A | G240D (GGC→GAC) | sdaC → | L‑serine:H(+) symporter SdaC |
| RA | 2,936,855 | T→G | A424A (GCT→GCG) | fucI → | L‑fucose isomerase |
| RA | 2,937,210 | C→T | L543F (CTC→TTC) | fucI → | L‑fucose isomerase |
| RA | 2,938,548 | A→T | T361S (ACG→TCG) | fucK → | L‑fuculokinase |
| RA | 2,945,282 | G→A | S187S (AGC→AGT) | tcdA ← | tRNA threonylcarbamoyladenosine dehydratase |
| RA | 2,946,310 | G→A | T290I (ACC→ATC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 2,954,917 | G→A | R363C (CGT→TGT) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,961,324 | G→A | P369S (CCA→TCA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,961,438 | G→A | P331S (CCA→TCA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,986,809 | G→A | Q321Q (CAG→CAA) | yqeG → | putative transporter YqeG |
| RA | 3,010,818 | G→A | C264Y (TGC→TAC) | hyuA → | phenylhydantoinase |
| RA | 3,018,087 | G→A | K676K (AAG→AAA) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,025,601 | (T)5→4 | coding (1251/1401 nt) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,070,858 | T→G | K129N (AAA→AAC) | fbaA ← | fructose‑bisphosphate aldolase class II |
| RA | 3,080,777 | G→T | P287T (CCG→ACG) | tktA ← | transketolase 1 |
| RA | 3,089,059 | A→T | Q259L (CAG→CTG) | galP → | galactose:H(+) symporter |
| RA | 3,179,064 | G→A | G317D (GGC→GAC) | tolC → | outer membrane channel TolC |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,227,963 | G→C | G55R (GGG→CGG) | ygjJ → | protein YgjJ |
| RA | 3,274,864 | G→A | T15I (ACC→ATC) | garP ← | galactarate/D‑glucarate transporter GarP |
| RA | 3,279,276 | C→G | F121L (TTC→TTG) | kbaZ → | putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone |
| RA | 3,296,481 | G→A | V25M (GTG→ATG) | dolP → | division and outer membrane stress‑associated lipid‑binding lipoprotein |
| RA | 3,319,301 | Δ1 bp | coding (665/1344 nt) | argG → | argininosuccinate synthetase |
| RA | 3,324,965 | G→T | intergenic (‑54/+36) | folP ← / ← ftsH | dihydropteroate synthase/ATP‑dependent zinc metalloprotease FtsH |
| RA | 3,326,537 | C→A | S133S (TCG→TCT) | ftsH ← | ATP‑dependent zinc metalloprotease FtsH |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,411,689 | G→T | E13* (GAA→TAA) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,433,900 | C→T | L71L (CTA→TTA) | def → | peptide deformylase |
| RA | 3,444,904 | C→T | G109D (GGT→GAT) | rpsE ← | 30S ribosomal subunit protein S5 |
| RA | 3,446,191 | C→T | A119T (GCT→ACT) | rpsH ← | 30S ribosomal subunit protein S8 |
| RA | 3,452,079 | A→T | S70T (TCT→ACT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,474,424 | T→G | K43N (AAA→AAC) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,486,502 | C→T | T128I (ACT→ATT) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,652 | G→C | G178A (GGC→GCC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,491,631 | C→A | intergenic (‑11/+94) | yhfG ← / ← ppiA | DUF2559 domain‑containing protein YhfG/peptidyl‑prolyl cis‑trans isomerase A |
| RA | 3,511,466 | C→T | V293V (GTG→GTA) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,555,047 | G→C | V655L (GTC→CTC) | malT → | DNA‑binding transcriptional activator MalT |
| MC JC | 3,555,171 | Δ11 bp | coding (2087‑2097/2706 nt) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,362 | G→A | intergenic (+496/+260) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,646,287 | G→A | intergenic (+60/‑12) | rlmJ → / → gor | 23S rRNA m(6)A2030 methyltransferase/glutathione reductase (NADPH) |
| RA | 3,647,428 | C→T | A377V (GCG→GTG) | gor → | glutathione reductase (NADPH) |
| RA | 3,653,066 | G→A | P33S (CCA→TCA) | insH11 ← | IS5 family transposase and trans‑activator |
| RA | 3,661,226 | G→A | G271G (GGG→GGA) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,663,006 | G→A | A865T (GCG→ACG) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,664,928 | G→A | noncoding (65/106 nt) | gadY → | small regulatory RNA GadY |
| RA | 3,688,359 | G→A | A272V (GCT→GTT) | bcsC ← | cellulose synthase outer membrane channel |
| RA | 3,689,787 | G→A | L159L (CTG→TTG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,692,266 | G→A | N114N (AAC→AAT) | bcsB ← | cellulose synthase periplasmic subunit |
| RA | 3,693,241 | G→A | L666F (CTC→TTC) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,715,926 | G→A | P157S (CCG→TCG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,719,429 | G→A | intergenic (‑385/‑49) | yiaF ← / → yiaG | DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG |
| RA | 3,720,794 | G→A | V39I (GTC→ATC) | insJ → | insertion element IS150 protein InsA |
| RA | 3,724,217 | G→A | L61L (CTG→TTG) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,729,440 | 2 bp→TT | noncoding (105‑106/160 nt) | xylZ ← | small RNA XylZ |
| RA | 3,730,083 | G→A | T228M (ACG→ATG) | xylA ← | xylose isomerase |
| RA | 3,730,560 | C→T | W69* (TGG→TAG) | xylA ← | xylose isomerase |
| RA | 3,739,696 | T→G | intergenic (+169/‑9) | malS → / → avtA | alpha‑amylase/valine‑‑pyruvate aminotransferase |
| RA | 3,746,267 | G→A | E58E (GAG→GAA) | yiaO → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ periplasmic binding protein |
| RA | 3,760,259 | G→A | L331F (CTC→TTC) | selA ← | selenocysteine synthase |
| RA | 3,770,539 | C→T | V281M (GTG→ATG) | yibH ← | inner membrane protein YibH |
| RA | 3,771,188 | G→A | I64I (ATC→ATT) | yibH ← | inner membrane protein YibH |
| RA | 3,773,173 | Δ1 bp | coding (893/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,773,176 | C→T | S299F (TCT→TTT) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,776,302 | C→T | E27K (GAG→AAG) | yibT ← | protein YibT |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,839,888 | C→T | V36I (GTT→ATT) | nlpA ← | lipoprotein‑28 |
| RA | 3,858,402 | C→T | M1M (ATG→ATA) † *572* (TGA→TAA) |
yidJ ← yidK ← |
putative sulfatase/phosphatase YidJ putative transporter YidK |
| RA | 3,914,237 | C→T | A322T (GCG→ACG) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | 3,926,991 | G→A | L5L (CTG→TTG) | asnC ← | DNA‑binding transcriptional dual regulator AsnC |
| RA | 3,936,392 | C→T | P39S (CCG→TCG) | rbsB → | ribose ABC transporter periplasmic binding protein |
| RA | 3,952,581 | G→A | G33D (GGC→GAC) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,956,495 | C→T | L389F (CTC→TTC) | ilvA → | threonine deaminase |
| RA | 3,966,530 | 2 bp→TT | coding (114‑115/1260 nt) | rho → | transcription termination factor Rho |
| RA | 3,969,914 | G→A | G295D (GGT→GAT) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,979,828 | G→A | V410I (GTC→ATC) | wzyE → | enterobacterial common antigen polymerase |
| RA | 3,982,060 | G→A | A392T (GCG→ACG) | yifK → | putative transporter YifK |
| RA | 3,993,808 | G→A | G84G (GGC→GGT) | cyaY ← | frataxin CyaY |
| RA | 3,993,970 | G→A | I30I (ATC→ATT) D41N (GAT→AAT) |
cyaY ← yzcX → |
frataxin CyaY protein YzcX |
| RA | 4,003,502 | G→T | P226Q (CCG→CAG) | rarD ← | putative transporter RarD |
| RA | 4,028,198 | G→A | T192I (ACC→ATC) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,028,589 | G→A | L62L (CTG→TTG) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,036,965 | G→A | noncoding (1435/1542 nt) | rrsA → | 16S ribosomal RNA |
| RA | 4,042,296 | C→T | F76F (TTC→TTT) | yihD → | DUF1040 domain‑containing protein YihD |
| RA | 4,057,018 | G→A | N339N (AAC→AAT) | glnA ← | glutamine synthetase |
| RA | 4,068,524 | G→A | D251D (GAC→GAT) | yihQ ← | sulfoquinovosidase |
| RA | 4,072,919 | G→A | T218I (ACT→ATT) | yihU ← | 3‑sulfolactaldehyde reductase |
| RA | 4,074,387 | G→A | G217S (GGC→AGC) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,077,794 | G→A | E116K (GAA→AAA) | fabY → | putative fatty acid biosynthesis enzyme FabY |
| RA | 4,080,171 | G→A | intergenic (+202/+128) | yiiF → / ← fdhE | protein YiiF/formate dehydrogenase formation protein |
| RA | 4,100,202 | G→A | G108G (GGC→GGT) | rhaT ← | rhamnose/lyxose:H(+) symporter |
| RA | 4,101,503 | G→A | intergenic (+73/‑187) | sodA → / → kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,102,164 | G→A | G159S (GGC→AGC) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,110,704 | G→A | intergenic (+19/+36) | cdh → / ← tpiA | CDP‑diacylglycerol diphosphatase/triose‑phosphate isomerase |
| RA | 4,111,879 | Δ1 bp | coding (336/600 nt) | yiiQ ← | DUF1454 domain‑containing protein YiiQ |
| RA | 4,119,232 | G→A | G33G (GGC→GGT) | rraA ← | ribonuclease E inhibitor protein A |
| JC JC | 4,123,617 | IS2 (–) +5 bp | coding (836‑840/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,132,781 | G→A | V56I (GTA→ATA) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,134,190 | G→A | G119D (GGC→GAC) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,150,418 | A→G | intergenic (‑153/+29) | eptC ← / ← ppc | phosphoethanolamine transferase EptC/phosphoenolpyruvate carboxylase |
| RA | 4,174,944 | G→A | P28L (CCT→CTT) | coaA ← | pantothenate kinase |
| RA | 4,184,802 | G→A | V1186V (GTG→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,199,100 | G→A | G104D (GGT→GAT) | nfi → | endonuclease V |
| RA | 4,203,291 | G→A | V456I (GTC→ATC) | zraS → | sensor histidine kinase ZraS |
| RA | 4,206,667 | G→A | A289V (GCC→GTC) | purH ← | bifunctional AICAR transformylase/IMP cyclohydrolase |
| RA | 4,214,979 | G→T | G234C (GGC→TGT) | metA → | homoserine O‑succinyltransferase |
| RA | 4,214,981 | C→T | G234C (GGC→TGT) | metA → | homoserine O‑succinyltransferase |
| RA | 4,217,310 | A→G | S68G (AGC→GGC) | aceA → | isocitrate lyase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,227,299 | G→A | E1158K (GAA→AAA) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,229,149 | G→A | L473L (TTG→TTA) | yjbB → | putative inorganic phosphate export protein YjbB |
| RA | 4,234,916 | G→A | A387T (GCG→ACG) | pgi → | glucose‑6‑phosphate isomerase |
| RA | 4,245,867 | G→A | P185S (CCG→TCG) | malE ← | maltose ABC transporter periplasmic binding protein |
| RA | 4,246,347 | G→A | L25F (CTC→TTC) | malE ← | maltose ABC transporter periplasmic binding protein |
| RA | 4,253,905 | G→A | intergenic (+17/+138) | ubiA → / ← plsB | 4‑hydroxybenzoate octaprenyltransferase/glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,255,799 | G→A | S223F (TCC→TTC) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,264,969 | C→G | A219G (GCT→GGT) | dnaB → | replicative DNA helicase |
| RA | 4,265,653 | G→A | G447E (GGG→GAG) | dnaB → | replicative DNA helicase |
| RA | 4,269,646 | G→A | S78N (AGT→AAT) | aphA → | acid phosphatase/phosphotransferase |
| RA | 4,272,615 | G→A | R419R (CGC→CGT) | uvrA ← | UvrABC excision nuclease subunit A |
| RA | 4,273,696 | G→A | A59V (GCC→GTC) | uvrA ← | UvrABC excision nuclease subunit A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,299,919 | G→A | A371V (GCC→GTC) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,331,890 | C→T | L463L (CTC→CTT) | proP → | osmolyte:H(+) symporter ProP |
| RA | 4,352,154 | G→A | V24I (GTC→ATC) | yjdJ → | putative N‑acetyltransferase YjdJ |
| RA | 4,359,223 | G→A | A270V (GCT→GTT) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,359,371 | G→A | P221S (CCG→TCG) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,363,999 | G→A | N348N (AAC→AAT) | dsbD ← | thiol‑disulfide exchange protein DsbD |
| RA | 4,364,490 | G→A | P185S (CCA→TCA) | dsbD ← | thiol‑disulfide exchange protein DsbD |
| RA | 4,397,469 | G→A | V20I (GTC→ATC) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,406,983 | C→T | L110L (CTC→CTT) | rnr → | RNase R |
| RA | 4,422,619 | G→A | G145D (GGC→GAC) | ulaD → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| RA | 4,434,584 | G→A | intergenic (+91/+38) | ytfH → / ← cpdB | putative transcriptional regulator YtfH/2',3'‑cyclic‑nucleotide 2'‑phosphodiesterase/3'‑nucleotidase |
| RA | 4,437,890 | C→T | Q62* (CAG→TAG) | ytfI → | protein YtfI |
| RA | 4,444,331 | G→A | A74T (GCG→ACG) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,453,174 | G→A | G202R (GGG→AGG) | ytfT → | galactofuranose ABC transporter putative membrane subunit YtfT |
| RA | 4,454,078 | G→A | G166R (GGA→AGA) | yjfF → | galactofuranose ABC transporter putative membrane subunit YjtF |
| RA | 4,455,185 | G→A | T142M (ACG→ATG) | fbp ← | fructose‑1,6‑bisphosphatase 1 |
| RA | 4,459,014 | G→A | R352R (CGG→CGA) | tldE → | metalloprotease subunit TldE |
| RA | 4,462,727 | G→A | intergenic (‑67/+327) | nrdD ← / ← treC | anaerobic ribonucleoside‑triphosphate reductase/trehalose‑6‑phosphate hydrolase |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,474,021 | G→A | I11I (ATC→ATT) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,474,056 | G→A | intergenic (‑3/‑68) | bdcA ← / → bdcR | c‑di‑GMP‑binding biofilm dispersal mediator protein/putative transcriptional regulator BdcR |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,476,605 | G→A | S390N (AGC→AAC) | yjgL → | protein YjgL |
| RA | 4,489,016 | C→T | E350K (GAA→AAA) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,494,603 | G→A | intergenic (‑197/‑20) | idnD ← / → idnK | L‑idonate 5‑dehydrogenase/D‑gluconate kinase, thermosensitive |
| RA | 4,499,294 | G→A | E234K (GAG→AAG) | insD6 → | IS2 insertion element protein InsB |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,513,267 | G→A | T48M (ACG→ATG) | fecC ← | ferric citrate ABC transporter membrane subunit FecC |
| RA | 4,518,062 | G→A | I58I (ATC→ATT) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,530,332 | G→A | L68F (CTT→TTT) | sgcB ← | putative PTS enzyme IIB component SgcB |
| JC JC | 4,542,042 | IS1 (+) +8 bp | coding (6‑13/597 nt) | fimE → | regulator for fimA |
| RA | 4,543,847 | G→A | A40A (GCG→GCA) | fimI → | putative fimbrial protein FimI |
| RA | 4,545,091 | G→A | intergenic (+62/‑5) | fimC → / → fimD | type 1 fimbriae periplasmic chaperone/type I fimbriae usher protein |
| RA | 4,545,646 | C→T | A184V (GCC→GTC) | fimD → | type I fimbriae usher protein |
| RA | 4,550,901 | G→A | A132A (GCC→GCT) | gntP ← | fructuronate transporter |
| RA | 4,554,876 | G→A | A101T (GCG→ACG) | uxuR → | DNA‑binding transcriptional repressor UxuR |
| RA | 4,608,611 | Δ1 bp | coding (427/447 nt) | rimI → | protein N‑acetyltransferase RimI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196245 | 1211460 | 15216 | 42 [40] | [41] 47 | [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 | 3423748–3424533 | 3424533 | 1–786 | 42 [41] | [41] 42 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 92 (0.840) | 83 (0.780) | 54/580 | 0.8 | 51.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 67 (0.630) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 100 (0.910) | 92 (0.870) | 62/580 | 0.5 | 52.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 67 (0.630) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||