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 | G→A | W282* (TGG→TAG) | 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 | 110,258 | C→T | Y660Y (TAC→TAT) | 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 | 292,019 | C→T | L174L (CTA→TTA) | yagJ → | protein YagJ |
| RA | 298,885 | G→A | P684S (CCG→TCG) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| 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 | 321,260 | A→T | intergenic (+179/‑348) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 365,306 | G→A | R334C (CGC→TGC) | lacZ ← | beta‑galactosidase |
| RA | 395,169 | C→T | E373E (GAG→GAA) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 400,444 | G→A | T160T (ACC→ACT) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 410,666 | C→T | P175S (CCT→TCT) | mak → | fructokinase |
| RA | 414,163 | G→A | R531* (CGA→TGA) | sbcC ← | ATP‑dependent structure‑specific DNA nuclease ‑ SbcC subunit |
| RA | 416,276 | G→A | A226V (GCA→GTA) | sbcD ← | ATP‑dependent structure‑specific DNA nuclease ‑ SbcD subunit |
| RA | 420,423 | G→A | G278D (GGC→GAC) | brnQ → | branched chain amino acid transporter BrnQ |
| RA | 421,027 | C→T | R14R (CGC→CGT) | proY → | putative transporter ProY |
| RA | 431,912 | C→T | W34* (TGG→TGA) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 465,005 | G→A | V181V (GTC→GTT) | queC ← | 7‑cyano‑7‑deazaguanine synthase |
| RA | 467,736 | G→A | G109S (GGT→AGT) | cof → | HMP‑PP phosphatase |
| RA | 471,709 | G→A | K358K (AAG→AAA) | mdlB → | ABC transporter family protein MdlB |
| 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 | 495,680 | C→T | F187F (TTC→TTT) | htpG → | chaperone protein HtpG |
| RA | 534,742 | G→A | G276D (GGT→GAT) | gcl → | glyoxylate carboligase |
| RA | 537,024 | C→T | P147S (CCG→TCG) | glxR → | tartronate semialdehyde reductase 2 |
| MC JC | 575,786 | Δ3,398 bp | IS5‑mediated | [nmpC]–borD | [nmpC], essD, rrrD, rzpD, rzoD, borD |
| RA | 582,597 | C→T | intergenic (+500/‑278) | tfaD → / → tfaX | putative tail fiber assembly protein TfaD/protein TfaX |
| RA | 627,348 | G→A | V427M (GTG→ATG) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| 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 | 708,774 | G→A | A147A (GCG→GCA) | chiP → | chitooligosaccharide outer membrane channel |
| RA | 721,604 | G→A | R44C (CGT→TGT) | kdpE ← | DNA‑binding transcriptional activator KdpE |
| RA | 753,977 | G→A | R164R (CGC→CGT) | gltA ← | citrate synthase |
| RA | 758,462 | G→A | intergenic (+57/‑244) | sdhB → / → sucA | succinate:quinone oxidoreductase, iron‑sulfur cluster binding protein/subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 780,624 | C→T | noncoding (71/76 nt) | lysT → | tRNA‑Lys |
| RA | 789,580 | C→A | E134* (GAA→TAA) | galK ← | galactokinase |
| JC JC | 820,914 | IS5 (+) +4 bp | coding (122‑125/714 nt) | ybhM → | Bax1‑I family protein YbhM |
| RA | 822,527 | C→T | E405K (GAA→AAA) | clsB ← | cardiolipin synthase B |
| 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 | 1,038,477 | 2 bp→AA | coding (738‑739/1545 nt) | appC → | cytochrome bd‑II subunit 1 |
| JC JC | 1,105,699 | IS1 (+) +9 bp | coding (286‑294/312 nt) | ymdA → | uncharacterized protein YmdA |
| RA | 1,123,823 | 2 bp→AG | coding (231‑232/648 nt) | grxB ← | reduced glutaredoxin 2 |
| JC JC | 1,125,587 | IS1 (+) +8 bp | coding (26‑33/585 nt) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,147,792 | T→A | S58T (TCG→ACG) | plsX → | putative phosphate acyltransferase |
| RA | 1,153,007 | G→A | A357T (GCG→ACG) | fabF → | 3‑oxoacyl‑[acyl carrier protein] synthase 2 |
| 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 | 1,196,245 | 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 |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,316 | T→A | D398E (GAT→GAA) | 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 | 1,290,518 | IS1 (–) +9 bp | coding (277‑285/1014 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 | 1,331,059 | 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 | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,395,367 | G→A | R186C (CGT→TGT) | ynaI ← | small conductance mechanosensitive channel YnaI |
| RA | 1,405,758 | G→A | intergenic (‑7/‑221) | mcaS ← / → smrA | small regulatory RNA McaS/DNA endonuclease SmrA |
| 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 |
|
| RA | 1,497,385 | 4 bp→CAA | coding (530‑533/1656 nt) | opgD → | glucans biosynthesis protein D |
| RA | 1,517,587 | 2 bp→TT | intergenic (+25/‑60) | ortT → / → ydcY | orphan toxin OrtT/DUF2526 domain‑containing protein YdcY |
| RA | 1,522,583 | C→T | Q161Q (CAG→CAA) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,541,037 | A→G | I518I (ATT→ATC) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,058 | G→A | T511T (ACC→ACT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,591,711 | C→A | E156* (GAG→TAG) | hipA ← | serine/threonine‑protein kinase toxin HipA |
| RA | 1,600,081 | C→T | W43* (TGG→TGA) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,629,247 | C→T | I11I (ATC→ATT) | ydfZ → | putative selenoprotein YdfZ |
| 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 | 1,660,102 | C→T | N678N (AAC→AAT) | ynfE → | putative selenate reductase YnfE |
| RA | 1,664,866 | C→T | Q121* (CAA→TAA) | dmsD → | redox enzyme maturation protein DmsD |
| RA | 1,667,460 | G→A | Q369* (CAG→TAG) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| JC | 1,744,735 | (ATT)2→1 | coding (1279‑1281/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,748,841 | C→T | R240K (AGA→AAA) | ydhT ← | uncharacterized protein YdhT |
| RA | 1,792,541 | C→T | G64E (GGA→GAA) | nlpC ← | NlpC/P60 family lipoprotein NlpC |
| RA | 1,799,792 | C→T | intergenic (‑43/+10) | rplT ← / ← rpmI | 50S ribosomal subunit protein L20/50S ribosomal subunit protein L35 |
| RA | 1,836,397 | G→A | E109K (GAG→AAG) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| RA | 1,848,300 | 2 bp→TT | coding (376‑377/552 nt) | ydjA ← | putative oxidoreductase YdjA |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,959,375 | G→A | P158S (CCG→TCG) | yecM ← | putative metal‑binding enzyme YecM |
| RA | 1,971,380 | C→T | E438K (GAA→AAA) | tar ← | methyl‑accepting chemotaxis protein Tar |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 1,979,987 | C→T | P79S (CCC→TCC) | uspC → | universal stress protein C |
| RA | 1,981,874 | C→T | G172S (GGT→AGT) | otsB ← | trehalose‑6‑phosphate phosphatase |
| RA | 1,987,212 | A→G | Q96Q (CAA→CAG) | ftnB → | putative ferritin‑like protein |
| RA | 1,993,143 | G→A | P522S (CCA→TCA) | uvrC ← | UvrABC excision nuclease subunit C |
| RA | 2,001,353 | T→C | Y146C (TAC→TGC) | fliA ← | RNA polymerase sigma factor FliA |
| RA | 2,002,825 | C→T | G261E (GGA→GAA) | fliC ← | flagellar filament structural protein |
| RA | 2,003,378 | T→C | T77A (ACC→GCC) | fliC ← | flagellar filament structural protein |
| RA | 2,021,904 | C→T | L12L (CTC→CTT) | fliP → | flagellar biosynthesis protein FliP |
| RA | 2,023,559 | A→G | T223A (ACT→GCT) | fliR → | flagellar biosynthesis protein FliR |
| RA | 2,026,636 | C→T | G461E (GGA→GAA) | dgcQ ← | diguanylate cyclase DgcQ |
| RA | 2,027,332 | T→A | E229V (GAA→GTA) | dgcQ ← | diguanylate cyclase DgcQ |
| 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 | 2,053,034 | C→T | intergenic (+1020/‑609) | yeeJ → / → shiA | inverse autotransporter adhesin/shikimate:H(+) symporter |
| RA | 2,060,006 | C→T | Q303Q (CAG→CAA) | cbl ← | DNA‑binding transcriptional activator Cbl |
| RA | 2,064,731 | C→T | R164R (CGG→CGA) | cobS ← | cobalamin 5'‑phosphate synthase |
| RA | 2,066,671 | C→T | Q205Q (CAG→CAA) | insH6 ← | IS5 family transposase and trans‑activator |
| RA | 2,066,707 | T→C | L193L (CTA→CTG) | insH6 ← | IS5 family transposase and trans‑activator |
| RA | 2,068,504 | C→T | intergenic (‑1219/‑131) | insH6 ← / → yoeA | IS5 family transposase and trans‑activator/TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,068,723 | C→T | pseudogene (89/306 nt) | yoeA → | TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,076,331 | C→T | L8L (CTC→CTT) | yeeS → | RadC‑like JAB domain‑containing protein YeeS |
| RA | 2,083,303 | C→T | A183V (GCG→GTG) | sbcB → | exodeoxyribonuclease I |
| RA | 2,090,780 | C→T | Q197* (CAA→TAA) | hisG → | ATP phosphoribosyltransferase |
| RA | 2,099,385 | C→T | V77I (GTC→ATC) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| 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 | 2,111,502 | C→T | G159R (GGA→AGA) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,112,656 | C→T | V136I (GTC→ATC) | rfbB ← | dTDP‑glucose 4,6‑dehydratase 1 |
| RA | 2,120,969 | G→A | L196L (CTG→TTG) | wcaJ ← | UDP‑glucose:undecaprenyl‑phosphate glucose‑1‑phosphate transferase |
| RA | 2,128,046 | C→T | S90N (AGC→AAC) | gmd ← | GDP‑mannose 4,6‑dehydratase |
| RA | 2,135,082 | C→T | A191T (GCC→ACC) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,140,209 | C→T | Q468Q (CAG→CAA) | asmA ← | putative assembly protein AsmA |
| RA | 2,142,598 | G→A | L117L (CTC→CTT) | udk ← | uridine/cytidine kinase |
| RA | 2,143,767 | C→T | L168L (CTG→TTG) | dgcE → | putative diguanylate cyclase DgcE |
| 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 |
| RA | 2,233,609 | C→T | Q4* (CAG→TAG) | yeiS → | DUF2542 domain‑containing protein YeiS |
| JC JC | 2,239,316 | IS5 (–) +4 bp | intergenic (‑27/+31) | mglA ← / ← mglB | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit/D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| 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 | 2,361,210 | C→G | E69Q (GAA→CAA) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,388,789 | C→T | P52L (CCG→CTG) | yfbO → | uncharacterized protein YfbO |
| RA | 2,404,402 | G→A | S71L (TCG→TTG) | nuoB ← | NADH:quinone oxidoreductase subunit B |
| RA | 2,481,608 | A→G | L190S (TTA→TCA) | emrY ← | tripartite efflux pump membrane subunit EmrY |
| RA | 2,498,392 | A→C | intergenic (‑97/‑279) | alaC ← / → pyrS | glutamate‑‑pyruvate aminotransferase AlaC/sensor histidine kinase PyrS |
| RA | 2,510,084 | C→T | S152F (TCT→TTT) | yfeO → | putative transport protein YfeO |
| RA | 2,518,927 | C→T | P39S (CCC→TCC) | yfeD → | putative DNA‑binding transcriptional regulator YfeD |
| RA | 2,520,199 | A→G | G158G (GGT→GGC) | gltX ← | glutamate‑‑tRNA ligase |
| RA | 2,522,441 | G→A | R13C (CGT→TGT) | xapR ← | DNA‑binding transcriptional activator XapR |
| RA | 2,524,090 | C→T | Q263Q (CAG→CAA) | xapA ← | xanthosine phosphorylase |
| RA | 2,528,150 | C→T | E4K (GAG→AAG) | ypeB ← | PF12843 family protein YpeB |
| RA | 2,533,306 | C→T | P300S (CCA→TCA) | cysK → | cysteine synthase A |
| RA | 2,535,491 | C→T | P476S (CCA→TCA) | ptsI → | PTS enzyme I |
| RA | 2,535,795 | C→T | intergenic (+2/‑39) | ptsI → / → crr | PTS enzyme I/Enzyme IIA(Glc) |
| RA | 2,540,538 | C→T | D93N (GAC→AAC) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,545,703 | C→T | intergenic (‑94/‑70) | murR ← / → murQ | DNA‑binding transcriptional dual regulator MurR/N‑acetylmuramic acid 6‑phosphate etherase |
| RA | 2,546,804 | T→A | D44E (GAT→GAA) | murP → | N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,567,007 | G→A | N367N (AAC→AAT) | eutH ← | putative ethanolamine permease EutH |
| RA | 2,570,269 | G→A | P23P (CCC→CCT) | eutJ ← | putative ethanolamine utilization chaperonin EutJ |
| RA | 2,577,291 | C→T | V363M (GTG→ATG) | maeB ← | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| RA | 2,577,937 | T→C | E147E (GAA→GAG) | maeB ← | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| RA | 2,585,210 | G→A | L106L (CTG→TTG) | aegA ← | putative oxidoreductase AegA |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,605,751 | G→A | G314D (GGC→GAC) | hyfD → | hydrogenase 4 component D |
| RA | 2,605,853 | G→A | G348D (GGT→GAT) | hyfD → | hydrogenase 4 component D |
| RA | 2,607,337 | G→A | A141T (GCG→ACG) | hyfF → | hydrogenase 4 component F |
| RA | 2,710,250 | G→A | intergenic (‑86/‑170) | rseD ← / → nadB | rpoE leader peptide/L‑aspartate oxidase |
| RA | 2,745,600 | A→G | Y107H (TAC→CAC) | rimM ← | ribosome maturation factor RimM |
| RA | 2,766,503 | G→A | D196N (GAT→AAT) | rnlA → | RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| 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 | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| JC JC | 2,955,094 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | coding (905‑910/3543 nt) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,959,564 | C→T | W955* (TGG→TGA) | recC ← | exodeoxyribonuclease V subunit RecC |
| 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 | 3,105,127 | G→A | G232E (GGA→GAA) | mltC → | membrane‑bound lytic murein transglycosylase C |
| RA | 3,148,900 | G→A | G335D (GGC→GAC) | gpr → | L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,167,046 | C→T | A225T (GCA→ACA) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,245,992 | G→A | V257I (GTT→ATT) | exuT → | hexuronate transporter |
| RA | 3,256,301 | G→A | S117S (TCC→TCT) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| 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 | 3,329,743 | 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 | 3,441,062 | G→A | S205F (TCC→TTC) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,486,175 | G→A | C19Y (TGC→TAC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,502 | C→T | T128I (ACT→ATT) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,489,288 | G→A | A298V (GCG→GTG) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,507,249 | C→T | D30N (GAC→AAC) | yhfT ← | uncharacterized protein YhfT |
| RA | 3,511,466 | C→T | V293V (GTG→GTA) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,522,616 | C→T | D46N (GAT→AAT) | hofM ← | DNA utilization protein HofM |
| RA | 3,526,801 | C→T | Y111Y (TAC→TAT) | igaA → | inner membrane protein IgaA |
| RA | 3,532,984 | C→T | A56V (GCC→GTC) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,555,047 | 2 bp→TG | coding (1963‑1964/2706 nt) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,555,371 | T→C | F763L (TTT→CTT) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,556,628 | C→T | Q74Q (CAG→CAA) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| 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 | 3,563,956 | C→T | G17D (GGC→GAC) | yzgL ← | putative uncharacterized protein YzgL |
| RA | 3,566,962 | C→T | A358T (GCA→ACA) | glgA ← | glycogen synthase |
| RA | 3,578,319 | C→T | K136K (AAG→AAA) | gntR ← | DNA‑binding transcriptional repressor GntR |
| RA | 3,581,238 | C→T | P34L (CCT→CTT) | yhhY → | N‑acetyltransferase YhhY |
| RA | 3,602,271 | C→T | L159L (CTG→CTA) | ftsE ← | cell division protein FtsE |
| RA | 3,608,348 | C→T | A633V (GCG→GTG) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,625,601 | C→T | intergenic (+87/+78) | yhhI → / ← yhhJ | putative transposase/ABC transporter family protein YhhJ |
| RA | 3,632,568 | C→T | G8D (GGC→GAC) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,633,558 | C→T | intergenic (‑968/‑1283) | yhiJ ← / → yhiM | DUF4049 domain‑containing protein YhiJ/inner membrane protein YhiM |
| RA | 3,637,711 | C→T | L24L (CTG→TTG) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,646,970 | G→T | Q224H (CAG→CAT) | gor → | glutathione reductase (NADPH) |
| RA | 3,647,428 | C→T | A377V (GCG→GTG) | gor → | glutathione reductase (NADPH) |
| RA | 3,648,339 | C→T | noncoding (46/82 nt) | agrB → | small regulatory RNA AgrB |
| MC JC | 3,653,231 | Δ4,600 bp | IS5‑mediated | yhiS–hdeD | yhiS, slp, dctR, yhiD, hdeB, hdeA, hdeD |
| RA | 3,658,873 | G→A | G170S (GGT→AGT) | gadE → | DNA‑binding transcriptional activator GadE |
| RA | 3,660,853 | G→A | G147D (GGC→GAC) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,661,547 | G→A | G378G (GGG→GGA) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,679,581 | G→A | G55R (GGA→AGA) | kdgK → | 2‑dehydro‑3‑deoxygluconokinase |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,719,429 | G→A | intergenic (‑385/‑49) | yiaF ← / → yiaG | DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG |
| 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 | 3,730,560 | C→T | W69* (TGG→TAG) | xylA ← | xylose isomerase |
| RA | 3,770,539 | C→T | V281M (GTG→ATG) | 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 | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,817,167 | C→T | T164T (ACC→ACT) | yicC → | putative RNase adaptor protein YicC |
| RA | 3,847,382 | C→T | V415I (GTT→ATT) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| RA | 3,866,958 | C→T | intergenic (‑61/+51) | ibpB ← / ← ibpA | small heat shock protein IbpB/small heat shock protein IbpA |
| RA | 3,880,366 | C→T | G286R (GGA→AGA) | recF ← | recombination mediator protein RecF |
| RA | 3,902,482 | C→T | S407N (AGT→AAT) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,926,991 | G→A | L5L (CTG→TTG) | asnC ← | DNA‑binding transcriptional dual regulator AsnC |
| RA | 3,931,779 | T→C | F155S (TTT→TCT) | kup → | K(+):H(+) symporter Kup |
| RA | 3,962,723 | C→T | intergenic (+25/+22) | rep → / ← gpp | ATP‑dependent DNA helicase Rep/guanosine‑5'‑triphosphate,3'‑diphosphate phosphatase |
| RA | 3,966,530 | 2 bp→TT | coding (114‑115/1260 nt) | rho → | transcription termination factor Rho |
| RA | 3,972,294 | C→T | I345I (ATC→ATT) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| RA | 3,986,856 | C→T | E343K (GAA→AAA) | hemY ← | protein HemY |
| RA | 3,993,093 | C→T | R647R (CGC→CGT) | cyaA → | adenylate cyclase |
| RA | 3,994,127 | C→T | T93I (ACC→ATC) | yzcX → | protein YzcX |
| RA | 3,998,170 | C→T | T63I (ACC→ATC) | uvrD → | DNA helicase II |
| RA | 3,998,612 | C→T | Y210Y (TAC→TAT) | uvrD → | DNA helicase II |
| RA | 3,999,260 | A→G | V426V (GTA→GTG) | uvrD → | DNA helicase II |
| RA | 4,003,380 | C→T | A267T (GCC→ACC) | rarD ← | putative transporter RarD |
| RA | 4,011,619 | C→T | L182L (CTG→TTG) | bioP → | biotin transporter |
| RA | 4,011,998 | C→T | Q273Q (CAG→CAA) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,014,732 | C→T | C560C (TGC→TGT) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,014,875 | C→T | P608L (CCG→CTG) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,018,102 | C→T | A257V (GCC→GTC) | rmuC → | putative recombination limiting protein RmuC |
| RA | 4,026,650 | G→A | D42N (GAT→AAT) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,029,121 | C→T | Q617Q (CAG→CAA) | fadB ← | multifunctional enoyl‑CoA hydratase, 3‑hydroxyacyl‑CoA epimerase, Delta(3)‑cis‑ Delta(2)‑trans‑enoyl‑CoA isomerase, L‑3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,030,999 | C→T | intergenic (‑28/‑162) | fadB ← / → pepQ | multifunctional enoyl‑CoA hydratase, 3‑hydroxyacyl‑CoA epimerase, Delta(3)‑cis‑ Delta(2)‑trans‑enoyl‑CoA isomerase, L‑3‑hydroxyacyl‑CoA dehydrogenase/Xaa‑Pro dipeptidase |
| RA | 4,038,003 | C→T | noncoding (485/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,046,693 | C→T | intergenic (‑91/‑273) | yihG ← / → polA | 1‑acylglycerol‑3‑phosphate O‑acyltransferase YihG/DNA polymerase I |
| RA | 4,055,494 | C→T | R282R (CGG→CGA) | glnL ← | protein histidine kinase NtrB |
| RA | 4,067,865 | C→T | G471D (GGC→GAC) | yihQ ← | sulfoquinovosidase |
| RA | 4,073,072 | C→T | G167E (GGG→GAG) | yihU ← | 3‑sulfolactaldehyde reductase |
| RA | 4,078,683 | C→T | intergenic (+245/‑608) | fabY → / → yiiE | putative fatty acid biosynthesis enzyme FabY/putative DNA‑binding transcriptional regulator YiiE |
| RA | 4,082,106 | G→A | G218G (GGC→GGT) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | 4,095,498 | C→T | C162Y (TGC→TAC) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,096,387 | C→T | R354R (CGG→CGA) | rhaB ← | rhamnulokinase |
| RA | 4,123,389 | C→T | intergenic (‑50/+42) | ftsN ← / ← cytR | cell division protein FtsN/DNA‑binding transcriptional repressor CytR |
| RA | 4,126,368 | C→T | G148D (GGC→GAC) | priA ← | primosomal protein N' |
| RA | 4,131,075 | A→G | Q414R (CAA→CGA) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,131,375 | G→A | R514H (CGC→CAC) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,132,065 | C→T | A744V (GCC→GTC) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,137,282 | C→T | E126K (GAA→AAA) | yijF ← | DUF1287 domain‑containing protein YijF |
| RA | 4,139,498 | C→T | E71K (GAA→AAA) | fsaB ← | fructose‑6‑phosphate aldolase 2 |
| RA | 4,140,761 | C→T | R487R (CGG→CGA) | ptsA ← | putative PTS multiphosphoryl transfer protein PtsA |
| RA | 4,146,192 | C→T | A733V (GCC→GTC) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,150,410 | C→T | intergenic (‑145/+37) | eptC ← / ← ppc | phosphoethanolamine transferase EptC/phosphoenolpyruvate carboxylase |
| RA | 4,153,836 | G→A | Q338* (CAA→TAA) | argE ← | acetylornithine deacetylase |
| RA | 4,154,616 | C→T | A78T (GCG→ACG) | argE ← | acetylornithine deacetylase |
| RA | 4,155,363 | C→T | T121T (ACC→ACT) | argC → | N‑acetylglutamylphosphate reductase |
| RA | 4,160,243 | C→T | G183D (GGT→GAT) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,171,557 | C→A | intergenic (+13/‑80) | rrlB → / → rrfB | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 4,184,500 | C→T | P1086S (CCT→TCT) | rpoB → | RNA polymerase subunit beta |
| RA | 4,187,828 | G→A | E827K (GAG→AAG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,215,670 | G→T | D65Y (GAT→TAT) | aceB → | malate synthase A |
| RA | 4,218,853 | C→T | Y86Y (TAC→TAT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,224,762 | G→A | G312D (GGC→GAC) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,225,271 | G→A | V482I (GTA→ATA) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,261,296 | C→T | S233L (TCG→TTG) | yjbM → | DUF2713 domain‑containing protein YjbM |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,306,660 | G→A | intergenic (‑63/+210) | yjcS ← / ← alsK | linear primary‑alkylsulfatase/D‑allose kinase |
| RA | 4,316,498 | G→A | H241Y (CAC→TAC) | phnM ← | RPnTP hydrolase |
| RA | 4,322,048 | (C)5→6 | coding (375/726 nt) | phnF ← | putative transcriptional regulator PhnF |
| 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 | 4,437,890 | C→T | Q62* (CAG→TAG) | ytfI → | protein YtfI |
| RA | 4,452,986 | C→T | A139V (GCC→GTC) | ytfT → | galactofuranose ABC transporter putative membrane subunit YtfT |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| 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 | 4,479,944 | G→A | G72E (GGG→GAG) | yjgN → | inner membrane protein YjgN |
| RA | 4,489,016 | C→T | E350K (GAA→AAA) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| JC JC | 4,586,822 | IS5 (+) +4 bp | intergenic (‑61/‑124) | hsdR ← / → mrr | type I restriction enzyme EcoKI endonuclease subunit/Type IV methyl‑directed restriction enzyme EcoKMrr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 255892 | 279980 | 24089 | 137 [0] | [22] 23 | gpt–insA2 | gpt,frsA,crl,insB9,insA9,crl,phoE,proB,proA,thrW,ykfI,yafW,ykfH,ykfG,yafX,ykfF,ykfB,yafY,yafZ,ykfA,perR,insN,insI1,insN,eyeA,ykfC,insH1,mmuP,mmuM,afuC,insB2,insA2 |
| * | * | ÷ | NC_000913 | 361657 | 362203 | 547 | 134 [1] | [0] 113 | [lacA]–[lacY] | [lacA],[lacY] |
| * | * | ÷ | NC_000913 | 1196323 | 1211460 | 15138 | 23 [22] | [22] 23 | [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 | 3130390–3131343 | 3132752 | 1410–2363 | 25 [22] | [22] 23 | [insH9]–[yghR] | [insH9],yghQ,[yghR] |
| * | * | ÷ | NC_000913 | 3423900–3424233 | 3424452–3424239 | 7–553 | 23 [22] | [22] 23 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035410–4035730 | 4036888–4035735 | 6–1479 | 24 [22] | [21] 23 | [rrsA] | [rrsA] |
| * | * | ÷ | NC_000913 | 4542050 | 4544734 | 2685 | 120 [1] | [0] 122 | [fimE]–[fimC] | [fimE],fimA,fimI,[fimC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 19796 = | NA (NA) | 133 (1.430) | 89/596 | 0.0 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 361656 | 0 (0.000) | coding (205/612 nt) | lacA | galactoside O‑acetyltransferase | |||||
| * | ? | NC_000913 | = 255891 | 0 (0.000) | 136 (1.450) | 96/598 | 0.0 | 100% | intergenic (‑175/‑86) | pepD/gpt | peptidase D/xanthine‑guanine phsophoribosyltransferase |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 113 (1.210) | 77/598 | 0.1 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 0 (0.000) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 100 (1.070) | 68/598 | 0.2 | 88.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 320902 = | 13 (0.140) | coding (676/855 nt) | rclR | DNA‑binding transcriptional activator RclR | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 101 (1.080) | 69/598 | 0.2 | 83.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3155677 = | 20 (0.210) | coding (323/1164 nt) | yqhD | NADPH‑dependent aldehyde reductase YqhD | |||||
| * | ? | NC_000913 | 3489050 = | 77 (0.830) | 21 (0.230) | 18/596 | 2.9 | 21.4% | coding (1131/1221 nt) | argD | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 119 (1.280) | 77/596 | 0.1 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 0 (0.000) | coding (13/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 122 (1.300) | 86/598 | 0.0 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4544735 = | 0 (0.000) | coding (432/726 nt) | fimC | type 1 fimbriae periplasmic chaperone | |||||