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 | 68,590 | G→A | Q487* (CAG→TAG) | araB ← | ribulokinase |
| RA | 134,196 | +T | coding (2582/2598 nt) | acnB → | AcnB |
| 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 |
| JC JC | 168,362 | IS1 (–) +9 bp | coding (879‑887/2244 nt) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 203,297 | G→A | V246V (GTG→GTA) | lpxA → | acyl‑[acyl‑carrier‑protein]‑‑UDP‑N‑ acetylglucosamine O‑acyltransferase |
| RA | 203,307 | A→T | T250S (ACC→TCC) | lpxA → | acyl‑[acyl‑carrier‑protein]‑‑UDP‑N‑ acetylglucosamine O‑acyltransferase |
| RA | 218,872 | G→A | intergenic (‑97/+15) | proS ← / ← trmO | proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase |
| JC JC | 233,968 | IS2 (+) +5 bp | intergenic (‑13/+55) | mltD ← / ← gloB | membrane‑bound lytic murein transglycosylase D/hydroxyacylglutathione hydrolase GloB |
| MC JC | 255,892 | Δ18,063 bp | IS5‑mediated | gpt–[ykfC] | 26 genes 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] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| 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 | 321,260 | A→T | intergenic (+179/‑348) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 322,812 | C→T | H159Y (CAT→TAT) | ykgF → | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain |
| RA | 348,736 | C→T | P19S (CCA→TCA) | prpB → | 2‑methylisocitrate lyase |
| JC JC | 362,204 | IS1 (–) +9 bp | coding (968‑976/1254 nt) | lacY ← | lactose permease |
| RA | 410,666 | C→T | P175S (CCT→TCT) | mak → | fructokinase |
| RA | 421,027 | C→T | R14R (CGC→CGT) | proY → | putative transporter ProY |
| JC JC | 431,643 | IS1 (+) +9 bp | coding (363‑371/885 nt) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 451,961 | T→A | intergenic (‑351/+109) | cyoA ← / ← ampG | cytochrome bo3 subunit 2/muropeptide:H(+) symporter |
| RA | 465,005 | G→A | V181V (GTC→GTT) | queC ← | 7‑cyano‑7‑deazaguanine synthase |
| RA | 472,849 | A→G | G84G (GGA→GGG) | glnK → | nitrogen regulatory protein PII‑2 |
| JC JC | 481,307 | IS1 (+) +8 bp | coding (3090‑3097/3150 nt) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 495,622 | C→T | T168I (ACC→ATC) | htpG → | chaperone protein HtpG |
| RA | 506,799 | G→A | S95L (TCG→TTG) | ybaK ← | Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
| RA | 534,742 | G→A | G276D (GGT→GAT) | gcl → | glyoxylate carboligase |
| 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 | 606,259 | C→T | intergenic (‑60/+6) | ybdJ ← / ← ybdK | DUF1158 domain‑containing protein YbdJ/putative glutamate‑‑cysteine ligase 2 |
| RA | 652,054 | (T)6→5 | intergenic (‑198/‑181) | citC ← / → dpiB | citrate lyase synthetase/sensor histidine kinase DpiB |
| 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 | 716,722 | C→T | intergenic (+816/+224) | ybfP → / ← potE | lipoprotein YbfP/putrescine transporter PotE |
| RA | 721,604 | G→A | R44C (CGT→TGT) | kdpE ← | DNA‑binding transcriptional activator KdpE |
| RA | 736,238 | Δ1 bp | intergenic (+19/‑207) | ybfC → / → ybfQ | uncharacterized protein YbfC/inactive transposase YbfQ |
| 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 | 900,653 | T→C | intergenic (‑78/+213) | artJ ← / ← artM | L‑arginine ABC transporter periplasmic binding protein/L‑arginine ABC transporter membrane subunit ArtM |
| RA | 908,169 | C→T | R38R (AGG→AGA) | ybjT ← | putative NAD(P)‑binding protein YbjT |
| MC JC | 989,673 | Δ8 bp | coding (677‑684/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,034,054 | G→T | T267T (ACG→ACT) | hyaB → | hydrogenase 1 large subunit |
| RA | 1,038,477 | 2 bp→AA | coding (738‑739/1545 nt) | appC → | cytochrome bd‑II subunit 1 |
| RA | 1,062,222 | G→A | E142K (GAG→AAG) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,078,792 | A→T | W31R (TGG→AGG) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,088,365 | Δ1 bp | coding (1493/2019 nt) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| 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 |
| RA | 1,147,300 | C→T | S169S (AGC→AGT) | yceD → | DUF177 domain‑containing protein YceD |
| 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 |
| JC JC | 1,186,408 | IS2 (–) +5 bp | coding (565‑569/1227 nt) | pepT → | peptidase T |
| 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 | 1,201,548 | A→C | T18P (ACC→CCA) | ymfI → | uncharacterized protein YmfI |
| RA | 1,201,550 | C→A | T18P (ACC→CCA) | ymfI → | uncharacterized protein YmfI |
| RA | 1,253,002 | C→T | intergenic (+17/+83) | dhaR → / ← ycgV | DNA‑binding transcriptional dual regulator DhaR/putative autotransporter adhesin YcgV |
| RA | 1,270,336 | C→T | A4T (GCG→ACG) | ldrC ← | small toxic polypeptide LdrC |
| RA | 1,275,021 | C→T | P413L (CCT→CTT) | ychO → | putative invasin YchO |
| JC JC | 1,293,196 | IS5 (+) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,301,164 | G→A | intergenic (+617/‑18) | insH21 → / → oppA | IS5 family transposase and trans‑activator/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 | 1,308,684 | T→C | intergenic (‑39/‑104) | clsA ← / → yciY | cardiolipin synthase A/uncharacterized protein YciY |
| RA | 1,320,154 | G→A | Q411* (CAA→TAA) | trpD ← | anthranilate synthase subunit TrpD |
| 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 | 1,382,603 | G→T | P219P (CCG→CCT) | ompG → | outer membrane porin G |
| 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 | 1,488,688 | A→G | N153D (AAC→GAC) | aldA → | aldehyde dehydrogenase A |
| RA | 1,497,385 | 4 bp→CAA | coding (530‑533/1656 nt) | opgD → | glucans biosynthesis protein D |
| RA | 1,505,527 | C→T | G185D (GGT→GAT) | ydcO ← | putative transport protein YdcO |
| RA | 1,515,161 | T→A | F134I (TTC→ATC) | ydcV → | putative ABC transporter membrane subunit YdcV |
| 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 | 1,629,247 | 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 | 1,667,460 | G→A | Q369* (CAG→TAG) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,682,877 | A→T | *240L (TAA→TTA) | rstA → | DNA‑binding transcriptional regulator RstA |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,748,841 | C→T | R240K (AGA→AAA) | ydhT ← | uncharacterized protein YdhT |
| RA | 1,757,981 | C→T | V249I (GTT→ATT) | ldtE ← | L,D‑transpeptidase LdtE |
| RA | 1,836,397 | G→A | E109K (GAG→AAG) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| RA | 1,843,473 | C→T | P368L (CCG→CTG) | gdhA → | glutamate dehydrogenase |
| RA | 1,848,300 | 2 bp→TT | coding (376‑377/552 nt) | ydjA ← | putative oxidoreductase YdjA |
| JC JC | 1,854,298 | IS5 (–) +4 bp | coding (554‑557/759 nt) | ydjF ← | putative DNA‑binding transcriptional regulator YdjF |
| RA | 1,860,493 | G→A | F280F (TTC→TTT) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,907,251 | G→T | A62E (GCA→GAA) | cspC ← | transcription antiterminator and regulator of mRNA stability CspC |
| RA | 1,956,004 | A→C | I335R (ATA→AGA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,968,630 | C→A | L245F (TTG→TTT) | cheR ← | chemotaxis protein methyltransferase |
| RA | 1,977,484 | A→G | W121R (TGG→CGG) | flhC ← | DNA‑binding transcriptional dual regulator FlhC |
| RA | 2,002,357 | G→A | A417V (GCT→GTT) | fliC ← | flagellar filament structural protein |
| RA | 2,023,559 | A→G | T223A (ACT→GCT) | fliR → | flagellar biosynthesis protein FliR |
| 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 | 2,043,488 | G→A | noncoding (70/90 nt) | serU ← | tRNA‑Ser |
| RA | 2,052,885 | G→A | intergenic (+871/‑758) | yeeJ → / → shiA | inverse autotransporter adhesin/shikimate:H(+) symporter |
| RA | 2,095,413 | G→A | A97T (GCG→ACG) | hisA → | 1‑(5‑phosphoribosyl)‑5‑[(5‑ phosphoribosylamino)methylideneamino]imidazole‑4‑ carboxamide isomerase |
| RA | 2,099,200 | G→A | F138F (TTC→TTT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,101,965 | G→A | A304V (GCG→GTG) | insH7 ← | IS5 family transposase and trans‑activator |
| RA | 2,110,045 | G→A | Q32* (CAA→TAA) | rfbC ← | dTDP‑4‑dehydrorhamnose 3,5‑epimerase |
| RA | 2,142,598 | G→A | L117L (CTC→CTT) | udk ← | uridine/cytidine kinase |
| RA | 2,144,705 | G→A | L480L (CTG→CTA) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,149,659 | G→A | Q443* (CAG→TAG) | yegI ← | putative serine/threonine‑protein kinase YegI |
| RA | 2,149,705 | G→T | I427I (ATC→ATA) | yegI ← | putative serine/threonine‑protein kinase YegI |
| 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 | 2,279,019 | G→A | P248S (CCG→TCG) | bcr ← | multidrug efflux pump Bcr |
| JC JC | 2,319,839 | IS2 (+) +5 bp | coding (34‑38/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,329,935 | C→T | intergenic (‑138/+4401) | yfaQ ← / ← yfaT | tandem DUF2300 domain‑containing protein YfaQ/DUF1175 domain‑containing protein YfaT |
| RA | 2,354,286 | A→C | M8L (ATG→CTG) | glpB → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B |
| RA | 2,389,456 | G→T | G114V (GGA→GTA) | yfbP → | uncharacterized protein YfbP |
| 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 | 2,517,590 | G→A | L81L (CTC→CTT) | pdeA ← | putative c‑di‑GMP phosphodiesterase PdeA |
| RA | 2,526,902 | A→C | intergenic (‑46/‑44) | yfeR ← / → yfeH | putative DNA‑binding transcriptional regulator YfeR/putative solute:Na(+) symporter |
| 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 | 2,577,937 | T→C | E147E (GAA→GAG) | maeB ← | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| RA | 2,584,265 | C→T | G421S (GGC→AGC) | aegA ← | putative oxidoreductase AegA |
| RA | 2,584,397 | +T | coding (1129/1980 nt) | aegA ← | putative oxidoreductase AegA |
| RA | 2,584,400 | C→A | D376Y (GAT→TAT) | aegA ← | putative oxidoreductase AegA |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| MC JC | 2,615,407 | Δ54 bp | coding (422‑475/1062 nt) | yfgO ← | putative transporter YfgO |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,745,600 | A→G | Y107H (TAC→CAC) | rimM ← | ribosome maturation factor RimM |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| RA | 2,781,539 | T→G | Q396H (CAA→CAC) | ypjA ← | adhesin‑like autotransporter YpjA |
| 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 | 2,893,657 | A→C | E334A (GAG→GCG) | ygcN → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,992,062 | C→A | intergenic (+303/‑32) | ygeG → / → ygeH | TPR repeat‑containing putative chaperone YgeG/putative transcriptional regulator YgeH |
| RA | 3,025,601 | (T)5→4 | coding (1251/1401 nt) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,043,140 | C→T | Q3Q (CAG→CAA) | yqfA ← | hemolysin‑III family protein YqfA |
| RA | 3,070,858 | T→G | K129N (AAA→AAC) | fbaA ← | fructose‑bisphosphate aldolase class II |
| MC JC | 3,131,341 | Δ128 bp | IS5‑mediated | yghQ ← | putative transport protein YghQ |
| RA | 3,147,115 | C→T | intergenic (‑378/+482) | yghW ← / ← yqhI | DUF2623 domain‑containing protein YghW/protein YqhI |
| RA | 3,194,816 | A→T | noncoding (50/145 nt) A17A (GCA→GCT) |
sibD ← ibsD → |
small RNA SibD putative toxic peptide IbsD |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,218,794 | C→T | V95M (GTG→ATG) | aer ← | aerotaxis receptor |
| RA | 3,227,355 | G→T | M374I (ATG→ATT) | ygjI → | putative transporter YgjI |
| JC JC | 3,261,756 | IS2 (+) +5 bp | coding (659‑663/2295 nt) | tdcE ← | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| RA | 3,275,902 | A→T | E207D (GAA→GAT) | garD → | GarD |
| 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 | 3,433,900 | C→T | L71L (CTA→TTA) | def → | peptide deformylase |
| RA | 3,444,923 | T→C | T103A (ACC→GCC) | rpsE ← | 30S ribosomal subunit protein S5 |
| 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 | 3,507,249 | 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 | 3,525,566 | T→C | intergenic (+143/+23) | mrcA → / ← nudE | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA/ADP‑sugar diphosphatase NudE |
| RA | 3,537,999 | C→T | F205F (TTC→TTT) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,553,214 | G→A | G44R (GGA→AGA) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,555,047 | G→T | V655F (GTC→TTC) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,582,181 | Δ1,247 bp | IS1‑mediated | [yhhZ]–[yrhA] | [yhhZ], [yrhA] |
| RA | 3,624,545 | T→A | D56E (GAT→GAA) | yhhI → | putative transposase |
| RA | 3,631,356 | 2 bp→AG | coding (1234‑1235/1623 nt) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| JC JC | 3,635,895 | IS1 (+) +9 bp | intergenic (+2/+305) | yhiM → / ← yhiN | inner membrane protein YhiM/putative oxidoreductase YhiN |
| RA | 3,647,428 | C→T | A377V (GCG→GTG) | gor → | glutathione reductase (NADPH) |
| RA | 3,677,528 | 2 bp→TT | coding (822‑823/2061 nt) | yhjG ← | AsmA family protein YhjG |
| RA | 3,679,508 | C→T | T30T (ACC→ACT) | kdgK → | 2‑dehydro‑3‑deoxygluconokinase |
| RA | 3,686,705 | G→A | F823F (TTC→TTT) | bcsC ← | cellulose synthase outer membrane channel |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,714,356 | A→T | I680K (ATA→AAA) | bisC ← | biotin sulfoxide reductase |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| 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 | 3,872,012 | Δ1 bp | coding (987/1149 nt) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,887,188 | C→T | L121F (CTT→TTT) | mnmE → | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,938,072 | C→T | A260V (GCG→GTG) | rbsK → | ribokinase |
| RA | 3,949,240 | C→T | E244K (GAG→AAG) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,953,602 | C→T | S42L (TCG→TTG) | ilvD → | dihydroxy‑acid dehydratase |
| RA | 3,961,662 | G→T | G329V (GGC→GTC) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,965,174 | G→A | H153Y (CAC→TAC) | rhlB ← | ATP‑dependent RNA helicase RhlB |
| RA | 3,968,683 | G→A | M256I (ATG→ATA) | rfe → | UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| RA | 3,969,748 | T→C | S240P (TCG→CCG) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,997,332 | G→A | Q50Q (CAG→CAA) | yigB → | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase |
| RA | 4,034,225 | C→T | L361L (CTG→TTG) | trkH → | K(+) transporter TrkH |
| RA | 4,048,596 | G→A | G544D (GGT→GAT) | polA → | DNA polymerase I |
| RA | 4,053,510 | C→T | intergenic (+92/+137) | hemN → / ← yshB | coproporphyrinogen III dehydrogenase/uncharacterized protein YshB |
| RA | 4,058,080 | C→T | intergenic (‑46/‑327) | glnA ← / → bipA | glutamine synthetase/50S ribosomal subunit assembly factor BipA |
| RA | 4,060,209 | C→T | N601N (AAC→AAT) | bipA → | 50S ribosomal subunit assembly factor BipA |
| RA | 4,061,758 | G→A | P198P (CCG→CCA) | yihM → | putative TIM barrel domain‑containing protein YihM |
| RA | 4,090,435 | Δ1 bp | coding (491/1071 nt) | frvX ← | peptidase M42 family protein FrvX |
| RA | 4,103,300 | T→A | L160Q (CTG→CAG) | yiiM → | 6‑hydroxyaminopurine reductase |
| RA | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| 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 | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| 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 | 4,366,023 | C→A | V251F (GTT→TTT) | dcuA ← | C4‑dicarboxylate transporter DcuA |
| RA | 4,422,299 | G→T | L38L (CTG→CTT) | ulaD → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| RA | 4,437,890 | C→T | Q62* (CAG→TAG) | ytfI → | protein YtfI |
| 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 | 4,489,016 | 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 |
| RA | 4,537,010 | G→A | H195H (CAC→CAT) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,537,018 | G→A | P193S (CCT→TCT) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,538,910 | Δ1 bp | coding (592/717 nt) | nanC ← | N‑acetylneuraminate outer membrane channel |
| RA | 4,566,834 | C→T | G138D (GGT→GAT) | yjiN ← | DUF445 domain‑containing protein YjiN |
| 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 | 1978484 | 1979270–1978503 | 20–787 | 35 [0] | [2] 32 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423870–3424234 | 3424438–3424238 | 5–569 | 8 [6] | [4] 7 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4542050 | 4555485 | 13436 | 44 [0] | [0] 51 | [fimE]–uxuR | [fimE],fimA,fimI,fimC,fimD,fimF,fimG,fimH,gntP,uxuA,uxuB,uxuR |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 11 (0.150) | 11/472 | 2.7 | 30.6% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1858973 = | 25 (0.340) | coding (1257/1380 nt) | ydjK | putative transporter YdjK | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 21 (0.280) | 20/476 | 1.8 | 55.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 923019 = | 17 (0.230) | coding (107/321 nt) | clpS | specificity factor for ClpA‑ClpP chaperone‑protease complex | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 26 (0.350) | 25/476 | 1.4 | 59.1% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 923023 | 18 (0.240) | coding (111/321 nt) | clpS | specificity factor for ClpA‑ClpP chaperone‑protease complex | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.470) | 14 (0.200) | 13/444 | 2.4 | 35.6% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 18 (0.260) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.410) | 51 (0.740) | 48/444 | 0.4 | 68.9% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 18 (0.260) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 23 (0.320) | 23/468 | 1.5 | 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 | 1638286 = | 11 (0.150) | 28 (0.380) | 25/476 | 1.4 | 71.8% | coding (159/189 nt) | ynfQ | protein YnfQ |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1638290 | 10 (0.140) | 17 (0.230) | 17/474 | 2.0 | 63.0% | coding (155/189 nt) | ynfQ | protein YnfQ |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1858745 = | 14 (0.190) | 15 (0.200) | 14/474 | 2.4 | 51.7% | coding (89/1044 nt) | ydjJ | putative zinc‑binding dehydrogenase YdjJ |
| ? | NC_000913 | 1978503 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1858752 | 15 (0.200) | 23 (0.310) | 20/476 | 1.8 | 60.5% | coding (82/1044 nt) | ydjJ | putative zinc‑binding dehydrogenase YdjJ |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1978483 | 0 (0.000) | 35 (0.470) | 33/476 | 1.0 | 100% | intergenic (‑286/+35) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 51 (0.690) | 51/476 | 0.4 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4555486 = | 0 (0.000) | intergenic (+137/+4) | uxuR/yjiC | DNA‑binding transcriptional repressor UxuR/DUF2686 domain‑containing protein YjiC | |||||
| * | ? | NC_000913 | 1979271 = | 2 (0.030) | 30 (0.430) +TTAAGTAATTGAGTG |
27/446 | 1.2 | 94.1% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (+2504/+12) | ygeI/insD4 | protein YgeI/IS2 insertion element protein InsB | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 44 (0.600) | 40/474 | 0.7 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 0 (0.000) | coding (13/597 nt) | fimE | regulator for fimA | |||||