mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 58,302 | T→G | intergenic (+123/‑172) | djlA → / → yabP | co‑chaperone protein DjlA/putative uncharacterized protein YabP |
| RA | 60,250 | A→G | L33L (TTG→CTG) | rluA ← | 23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase |
| RA | 76,877 | A→G | R141R (CGT→CGC) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 94,350 | T→C | R395R (CGT→CGC) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 157,738 | A→G | G463G (GGT→GGC) | pcnB ← | poly(A) polymerase I |
| RA | 169,237 | A→G | D585G (GAC→GGC) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 218,835 | (A)8→9 | intergenic (‑60/+52) | proS ← / ← trmO | proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase |
| RA | 236,132 | T→C | G22G (GGT→GGC) | dnaQ → | DNA polymerase III subunit epsilon |
| RA | 252,978 | T→C | R90R (CGT→CGC) | yafP → | putative acyltransferase with acyl‑CoA N‑acyltransferase domain |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 266,477 | T→C | D26G (GAT→GGT) | yafY ← | CP4‑6 prophage; inner membrane lipoprotein YafY |
| RA | 267,569 | A→G | V146A (GTG→GCG) | yafZ ← | CP4‑6 prophage; conserved protein YafZ |
| RA | 276,001 | C→T | A226V (GCC→GTC) | mmuP → | S‑methyl‑L‑methionine transporter |
| RA | 279,941 | Δ1 bp | intergenic (‑66/+444) | insA‑2 ← / ← yagB | IS1 protein InsA/orphan antitoxin YagB |
| RA | 293,637 | T→C | Q94Q (CAA→CAG) | yagL ← | CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL |
| RA | 300,630 | C→T | G102D (GGC→GAC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 341,258 | A→G | N45S (AAC→AGC) | yahJ → | putative deaminase with metallo‑dependent hydrolase domain |
| RA | 366,110 | C→T | A66T (GCA→ACA) | lacZ ← | beta‑galactosidase |
| RA | 370,051 | A→G | T481A (ACC→GCC) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 390,331 | A→G | pseudogene (81/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 393,275 | T→C | pseudogene (306/1449 nt) | yaiT → | putative autotransporter YaiT |
| RA | 394,868 | G→A | W121* (TGG→TGA) | iprA → | putative DNA‑binding transcriptional regulator IprA |
| RA | 407,061 | A→G | Y28C (TAC→TGC) | yaiA → | protein YaiA |
| RA | 447,812 | T→C | T79A (ACG→GCG) | cyoD ← | cytochrome bo3 ubiquinol oxidase subunit 4 |
| RA | 460,324 | A→G | A479A (GCA→GCG) | lon → | Lon protease |
| JC | 472,742 | (G)6→9 | coding (145/339 nt) | glnK → | nitrogen regulator GlnK |
| RA | 479,422 | A→G | V166A (GTC→GCC) | maa ← | maltose O‑acetyltransferase |
| RA | 524,518 | G→T | A420S (GCG→TCG) | rhsD → | protein RhsD |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 535,831 | A→G | D41G (GAC→GGC) | hyi → | hydroxypyruvate isomerase |
| RA | 542,669 | T→C | L261P (CTC→CCC) | glxK → | glycerate 2‑kinase 2 |
| RA | 590,918 | A→G | S13P (TCT→CCT) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 596,751 | T→C | R384R (CGT→CGC) | cusC → | copper/silver export system outer membrane channel |
| RA | 614,854 | A→G | D233G (GAC→GGC) | entF → | apo‑serine activating enzyme |
| RA | 657,119 | A→G | intergenic (+2/‑173) | pagP → / → cspE | Lipid IVA palmitoyltransferase/transcription antiterminator and regulator of RNA stability |
| RA | 694,215 | A→G | D247D (GAT→GAC) | miaB ← | isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 699,726 | C→T | D201N (GAT→AAT) | umpH ← | UMP phosphatase |
| RA | 701,932 | C→T | A274T (GCC→ACC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
| RA | 731,035 | A→T | I485M (ATA→TTG) | rhsC → | rhs element protein RhsC |
| RA | 731,037 | A→G | I485M (ATA→TTG) | rhsC → | rhs element protein RhsC |
| RA | 731,982 | C→T | G800G (GGC→GGT) | rhsC → | rhs element protein RhsC |
| RA | 731,984 | 2 bp→AC | coding (2402‑2403/4194 nt) | rhsC → | rhs element protein RhsC |
| RA | 731,989 | T→G | S803A (TCA→GCA) | rhsC → | rhs element protein RhsC |
| MC JC | 770,007 | Δ36 bp | coding (2030‑2065/2634 nt) | mngB → | alpha‑mannosidase |
| RA | 773,511 | A→G | Y157C (TAC→TGC) | cydB → | cytochrome bd‑I ubiquinol oxidase subunit II |
| RA | 778,928 | A→G | M397V (ATG→GTG) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 801,849 | A→G | intergenic (+38/‑38) | ybhH → / → ybhI | putative isomerase YbhH/putative tricarboxylate transporter |
| RA | 832,792 | T→C | A53A (GCA→GCG) | ybiA ← | N‑glycosidase YbiA |
| RA | 842,966 | A→G | D212G (GAT→GGT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase |
| RA | 858,019 | (G)5→6 | coding (1043/1266 nt) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 866,548 | A→G | intergenic (‑184/‑20) | moeA ← / → iaaA | molybdopterin molybdotransferase/isoaspartyl dipeptidase proenzyme |
| RA | 871,446 | C→T | G160G (GGC→GGT) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 880,940 | A→G | T72A (ACC→GCC) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 894,968 | A→G | intergenic (+72/‑23) | potF → / → potG | putrescine ABC transporter periplasmic binding protein/putrescine ABC transporter ATP binding subunit |
| RA | 897,059 | A→G | Q309R (CAG→CGG) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 902,802 | T→C | T63A (ACT→GCT) | artI ← | putative ABC transporter periplasmic binding protein ArtI |
| RA | 907,602 | A→G | G227G (GGT→GGC) | ybjT ← | putative NAD(P)‑dependent oxidoreductase YbjT |
| RA | 915,196 | T→C | intergenic (‑339/+156) | lysO ← / ← aqpZ | L‑lysine exporter/water channel AqpZ |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 946,269 | T→C | A133A (GCT→GCC) | ycaD → | putative transporter YcaD |
| RA | 950,923 | A→G | V53A (GTT→GCT) | pflA ← | pyruvate formate‑lyase activating enzyme |
| RA | 995,271 | A→G | W240R (TGG→CGG) | ssuD ← | FMNH2‑dependent alkanesulfonate monooxygenase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,018,976 | (A)8→9 | intergenic (+39/+37) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,048,907 | A→G | S142S (AGT→AGC) | gfcB ← | lipoprotein GfcB |
| RA | 1,057,881 | T→C | E25G (GAG→GGG) | torR ← | DNA‑binding transcriptional dual regulator TorR |
| RA | 1,107,290 | A→G | L312L (CTA→CTG) | clsC → | cardiolipin synthase C |
| RA | 1,113,143 | A→G | T761A (ACC→GCC) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,122,625 | C→T | intergenic (‑18/+88) | pyrC ← / ← yceB | dihydroorotase/putative lipid‑binding lipoprotein YceB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,146,273 | A→G | L108S (TTG→TCG) | yceF ← | m(7)GTP pyrophosphatase |
| RA | 1,157,840 | (A)7→6 | intergenic (+266/‑29) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,187,833 | A→G | G136G (GGT→GGC) | roxA ← | ribosomal protein‑arginine oxygenase |
| RA | 1,190,955 | A→G | R344R (CGT→CGC) | purB ← | adenylosuccinate lyase |
| RA | 1,203,536 | A→G | D90G (GAC→GGC) | ymfL → | e14 prophage; uncharacterized protein YmfL |
| RA | 1,207,942 | (G)7→8 | coding (442/630 nt) | ycfK → | e14 prophage; protein StfP |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,215,964 | A→G | H59R (CAC→CGC) | ycgZ → | putative two‑component system connector protein YcgZ |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,221,495 | (G)5→6 | pseudogene (1895/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,235,072 | T→C | R45R (CGT→CGC) | fadR → | DNA‑binding transcriptional dual regulator FadR |
| RA | 1,276,245 | C→T | E458E (GAG→GAA) | narX ← | sensory histidine kinase NarX |
| RA | 1,302,015 | G→A | L278L (TTG→TTA) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,336,475 | C→T | T215T (ACC→ACT) | acnA → | aconitate hydratase 1 |
| RA | 1,347,071 | A→G | G614G (GGT→GGC) | rnb ← | RNase II |
| RA | 1,354,843 | A→G | Y210H (TAT→CAT) | sapB ← | putrescine ABC exporter membrane subunit SapB |
| RA | 1,361,982 | T→C | R24R (CGT→CGC) | puuR → | DNA‑binding transcriptional repressor PuuR |
| RA | 1,396,097 | A→G | R8G (AGA→GGA) | insH‑4 → | IS5 transposase and trans‑activator |
| RA | 1,412,277 | G→A | P320L (CCC→CTC) | intR ← | Rac prophage; putative integrase |
| RA | 1,420,793 | (G)6→5 | coding (110/423 nt) | ydaT → | Rac prophage; protein YdaT |
| RA | 1,447,390 | C→T | intergenic (‑107/‑129) | feaR ← / → feaB | DNA‑binding transcriptional activator FeaR/phenylacetaldehyde dehydrogenase |
| RA | 1,456,663 | A→G | G78G (GGA→GGG) | paaE → | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| RA | 1,458,625 | (G)6→7 | coding (362/789 nt) | paaG → | putative ring 1,2‑epoxyphenylacetyl‑CoA isomerase (oxepin‑CoA forming) |
| RA | 1,499,780 | C→T | A224T (GCC→ACC) | ydcK ← | putative enzyme YdcK |
| RA | 1,515,125 | A→G | T122A (ACC→GCC) | ydcV → | putative ABC transporter membrane subunit YdcV |
| JC | 1,533,857 | +TATC | intergenic (‑6/‑167) | yddH ← / → nhoA | flavin reductase‑like protein YddH/arylamine N‑acetyltransferase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,569,312 | A→G | V393A (GTT→GCT) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,584,678 | +A | coding (1809/2280 nt) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,633 | T→C | pseudogene (3454/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,632,770 | T→C | intergenic (‑485/‑120) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,632,837 | A→G | intergenic (‑552/‑53) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,632,949 | C→T | A20A (GCC→GCT) | ynfT → | Qin prophage; protein YnfT |
| RA | 1,639,896 | A→G | G54G (GGT→GGC) | rrrQ ← | Qin prophage; putative lysozyme |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,694,138 | A→G | G42G (GGT→GGC) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,709,415 | (C)7→9 | coding (274/1059 nt) | rsxD → | SoxR [2Fe‑2S] reducing system protein RsxD |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,721,159 | T→C | R45R (CGT→CGC) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,727,494 | (G)6→8 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,730,557 | C→T | P491S (CCG→TCG) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,742,242 | T→C | V277A (GTT→GCT) | cfa → | cyclopropane fatty acyl phospholipid synthase |
| RA | 1,784,262 | G→A | G429D (GGC→GAC) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,813,656 | T→C | K3R (AAA→AGA) | cedA ← | cell division modulator |
| RA | 1,866,080 | A→G | D131D (GAT→GAC) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| RA | 1,871,508 | G→A | W375* (TGG→TAG) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,903,423 | T→C | R114R (CGT→CGC) | manY → | mannose‑specific PTS enzyme IIC component |
| RA | 1,904,364 | T→C | V157A (GTG→GCG) | manZ → | mannose‑specific PTS enzyme IID component |
| RA | 1,944,255 | T→C | intergenic (+56/+91) | znuB → / ← ruvB | Zn(2(+)) ABC transporter membrane subunit/Holliday junction branch migration complex subunit RuvB |
| RA | 1,974,645 | T→C | E227G (GAA→GGA) | cheA ← | chemotaxis protein CheA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,106 | (C)6→7 | intergenic (‑147/‑116) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 1,993,987 | G→A | T240T (ACC→ACT) | uvrC ← | excision nuclease subunit C |
| RA | 1,995,334 | T→C | D9G (GAC→GGC) | uvrY ← | DNA‑binding transcriptional activator UvrY |
| RA | 2,073,574 | A→G | N679S (AAC→AGC) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,137,892 | Δ1 bp | intergenic (‑649/‑10) | wza ← / → yegH | outer membrane polysaccharide export protein Wza/inner membrane protein YegH |
| RA | 2,167,478 | T→C | T15A (ACA→GCA) | ogrK ← | prophage P2 late control protein OgrK |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,194,993 | A→G | I232V (ATC→GTC) | metG → | methionine‑‑tRNA ligase |
| RA | 2,230,727 | C→T | T35I (ACC→ATC) | yohJ → | PF03788 family membrane protein YohJ |
| RA | 2,258,737 | T→C | N187S (AAC→AGC) | psuK ← | putative pseudouridine kinase |
| RA | 2,281,874 | T→C | F415L (TTT→CTT) | radD → | putative DNA repair helicase RadD |
| RA | 2,299,683 | (T)5→4 | coding (578/696 nt) | napG ← | ferredoxin‑type protein NapG |
| RA | 2,305,810 | T→C | K315K (AAA→AAG) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,307,612 | T→G | N335T (AAC→ACC) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,320,303 | (C)5→4 | coding (261/1827 nt) | atoS → | sensory histidine kinase AtoS |
| RA | 2,368,443 | G→A | M135I (ATG→ATA) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,373,161 | T→C | A90A (GCT→GCC) | arnF → | undecaprenyl‑phosphate‑alpha‑L‑Ara4N flippase ‑ ArnF subunit |
| RA | 2,381,909 | T→C | V101A (GTG→GCG) | rbn → | ribonuclease BN |
| RA | 2,400,895 | T→C | T221A (ACC→GCC) | nuoF ← | NADH:quinone oxidoreductase subunit F |
| RA | 2,405,417 | (C)6→7 | intergenic (‑345/+286) | nuoA ← / ← lrhA | NADH:quinone oxidoreductase subunit A/DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,425,237 | T→C | D227G (GAC→GGC) | hisQ ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ |
| RA | 2,426,785 | (T)6→7 | coding (4/783 nt) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,472,070 | T→C | intergenic (‑8/+42) | yfdL ← / ← yfdM | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL/CPS‑53 (KpLE1) prophage; putative methyltransferase |
| RA | 2,474,455 | T→C | W142R (TGG→CGG) | yfdQ → | CPS‑53 (KpLE1) prophage; protein YfdQ |
| RA | 2,478,169 | T→C | V108A (GTT→GCT) | dsdX → | D‑serine transporter |
| RA | 2,518,470 | A→G | T2A (ACA→GCA) | yfeC → | putative DNA‑binding transcriptional regulator YfeC |
| RA | 2,526,791 | A→G | R22R (CGT→CGC) | yfeR ← | putative LysR‑type DNA‑binding transcriptional regulator YfeR |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,552,141 | T→C | intergenic (‑3/‑211) | ypeA ← / → amiA | putative acetyltransferase YpeA/N‑acetylmuramoyl‑L‑alanine amidase A |
| RA | 2,552,558 | T→C | D69D (GAT→GAC) | amiA → | N‑acetylmuramoyl‑L‑alanine amidase A |
| RA | 2,564,534 | A→G | E4E (GAA→GAG) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,565,560 | T→C | D442G (GAC→GGC) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,604,561 | G→A | A239T (GCA→ACA) | hyfC → | hydrogenase 4 component C |
| RA | 2,626,471 | A→G | T453A (ACC→GCC) | ppx → | exopolyphosphatase |
| RA | 2,646,583 | (G)6→5 | coding (743/2313 nt) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,725,721 | T→C | D9G (GAC→GGC) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,744,611 | T→C | E243E (GAA→GAG) | trmD ← | tRNA m(1)G37 methyltransferase |
| RA | 2,747,069 | T→C | T243A (ACC→GCC) | ffh ← | signal recognition particle protein component |
| RA | 2,754,863 | T→C | intergenic (‑99/‑33) | ratA ← / → smpB | ribosome association toxin RatA/SsrA‑binding protein |
| RA | 2,768,347 | G→A | C213Y (TGT→TAT) | yfjP → | CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,786,623 | (A)6→5 | pseudogene (227/2253 nt) | ygaQ → | putative uncharacterized protein YgaQ |
| RA | 2,790,141 | G→A | V54I (GTC→ATC) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,844,595 | T→C | N53S (AAC→AGC) | hycF ← | formate hydrogenlyase subunit HycF |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,861,229 | T→C | I2M (ATA→ATG) | ygbI ← | putative DeoR‑type DNA‑binding transcriptional regulator YgbI |
| RA | 2,863,460 | T→C | F376L (TTT→CTT) | ygbK → | putative 3‑oxo‑tetronate kinase YgbK |
| RA | 2,890,515 | T→C | T462A (ACC→GCC) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,894,436 | A→G | T81A (ACC→GCC) | ygcP → | putative anti‑terminator regulatory protein |
| RA | 2,911,200 | A→G | V47A (GTG→GCG) | mazE ← | antitoxin of the MazF‑MazE toxin‑antitoxin system MazE |
| RA | 2,935,949 | A→G | A122A (GCA→GCG) | fucI → | L‑fucose isomerase |
| RA | 2,949,236 | T→C | intergenic (‑226/‑6) | amiC ← / → argA | N‑acetylmuramoyl‑L‑alanine amidase C/N‑acetylglutamate synthase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,953,839 | G→A | A722V (GCC→GTC) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,966,109 | G→A | intergenic (‑72/+79) | lgt ← / ← ptsP | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase/phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,968,718 | T→C | D87G (GAC→GGC) | rppH ← | RNA pyrophosphohydrolase |
| RA | 2,988,019 | T→C | Y162H (TAT→CAT) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,006,352 | A→G | T31A (ACG→GCG) | ygeW → | putative carbamoyltransferase YgeW |
| RA | 3,016,733 | T→C | L225P (CTC→CCC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,021,444 | Δ1 bp | coding (129/2871 nt) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,031,583 | Δ1 bp | coding (217/1449 nt) | uacT → | urate:H(+) symporter |
| RA | 3,033,157 | A→G | L31L (TTA→TTG) | idi → | isopentenyl‑diphosphate Delta‑isomerase |
| RA | 3,045,619 | T→C | T95A (ACC→GCC) | ygfF ← | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,081,892 | A→G | intergenic (‑257/‑21) | tktA ← / → loiP | transketolase 1/metalloprotease LoiP |
| RA | 3,093,919 | C→T | intergenic (+3/+181) | yqgF → / ← yggR | ribonuclease H‑like domain containing nuclease/Type II/IV secretion system family protein |
| RA | 3,095,346 | C→T | G83G (GGC→GGT) | yggS → | PLP homeostasis protein |
| RA | 3,101,067 | T→C | N186S (AAC→AGC) | yggN ← | putative EcfF |
| RA | 3,109,075 | A→G | D27D (GAT→GAC) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,119,973 | G→A | S436F (TCC→TTC) | glcA ← | glycolate/lactate:H(+) symporter GlcA |
| RA | 3,139,399 | T→C | Y225H (TAT→CAT) | yghU → | disulfide reductase/organic hydroperoxide reductase |
| RA | 3,148,428 | (A)6→7 | coding (532/1041 nt) | gpr → | L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,153,839 | T→C | L93L (TTA→CTA) | yghB → | DedA family protein YghB |
| RA | 3,157,712 | (C)6→7 | coding (63/927 nt) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,165,384 | T→C | D197G (GAC→GGC) | parC ← | DNA topoisomerase IV subunit A |
| RA | 3,180,279 | T→C | V179A (GTA→GCA) | ygiB → | DUF1190 domain‑containing protein YgiB |
| RA | 3,181,931 | C→T | M168I (ATG→ATA) | ygiD ← | 4,5‑DOPA dioxygenase extradiol |
| RA | 3,203,779 | T→C | N118S (AAC→AGC) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,210,821 | T→C | V14A (GTA→GCA) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,238,460 | A→G | intergenic (+163/‑120) | ygjR → / → alx | putative oxidoreductase YgjR/putative membrane‑bound redox modulator Alx |
| RA | 3,245,550 | T→C | G109G (GGT→GGC) | exuT → | hexuronate transporter |
| RA | 3,270,488 | (C)7→9 | noncoding (105/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,286,059 | T→C | H194H (CAT→CAC) | agaD → | galactosamine‑specific PTS enzyme IID component |
| RA | 3,291,477 | A→G | N46S (AAC→AGC) | yraK → | putative fimbrial adhesin YraK |
| RA | 3,301,885 | A→G | D134G (GAC→GGC) | yhbU → | putative peptidase YhbU |
| RA | 3,337,780 | T→C | T38A (ACG→GCG) | mlaC ← | intermembrane phospholipid transport system ‑ periplasmic binding protein |
| RA | 3,344,042 | T→C | G33G (GGT→GGC) | lptB → | lipopolysaccharide transport system ATP binding protein |
| RA | 3,348,053 | T→C | F30L (TTT→CTT) | npr → | phosphorelay protein Npr |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,373,324 | T→C | T85A (ACC→GCC) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,400,773 | A→G | R105R (CGT→CGC) | mreB ← | dynamic cytoskeletal protein MreB |
| RA | 3,413,816 | T→C | intergenic (‑351/‑48) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,424,645 | A→G | noncoding (2139/2904 nt) | rrlD ← | 23S ribosomal RNA |
| RA | 3,426,921 | A→G | intergenic (‑138/+37) | rrlD ← / ← alaU | 23S ribosomal RNA/tRNA‑Ala |
| RA | 3,428,808 | T→C | intergenic (‑46/‑428) | rrsD ← / → yrdA | 16S ribosomal RNA/protein YrdA |
| RA | 3,467,767 | T→C | D696G (GAC→GGC) | chiA ← | endochitinase |
| RA | 3,475,019 | G→A | A105V (GCC→GTC) | tusC ← | sulfurtransferase complex subunit TusC |
| RA | 3,537,315 | G→A | intergenic (+27/‑70) | greB → / → yhgF | transcription elongation factor GreB/putative RNA‑binding protein YhgF |
| RA | 3,537,763 | G→A | A127T (GCT→ACT) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,541,770 | T→C | V455A (GTC→GCC) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,576,646 | T→C | N139S (AAC→AGC) | gntU ← | low‑affinity gluconate transporter |
| RA | 3,625,168 | T→C | V264A (GTC→GCC) | yhhI → | putative transposase |
| RA | 3,631,981 | T→C | T204A (ACC→GCC) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,650,871 | T→C | intergenic (+209/‑420) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,668,544 | (C)6→7 | coding (645/1398 nt) | ccp ← | cytochrome c peroxidase |
| RA | 3,676,025 | G→A | V414M (GTG→ATG) | yhjE → | putative transporter YhjE |
| RA | 3,683,474 | T→C | intergenic (‑27/+156) | dctA ← / ← pdeK | C4 dicarboxylate/orotate:H(+) symporter/putative c‑di‑GMP phosphodiesterase PdeK |
| RA | 3,692,951 | Δ1 bp | coding (2286/2619 nt) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,714,076 | T→C | V142A (GTG→GCG) P773P (CCA→CCG) |
yiaC → bisC ← |
putative acyltransferase with acyl‑CoA N‑acyltransferase domain biotin sulfoxide reductase |
| RA | 3,735,669 | G→A | A231T (GCC→ACC) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| RA | 3,739,696 | T→C | intergenic (+169/‑9) | malS → / → avtA | alpha‑amylase/valine‑‑pyruvate aminotransferase |
| RA | 3,772,697 | G→A | G139G (GGG→GGA) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,812,130 | T→C | T144A (ACG→GCG) | yicR ← | RadC‑like JAB domain‑containing protein YicR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,818,975 | T→C | I34I (ATT→ATC) | yicG → | conserved inner membrane protein YicG |
| RA | 3,834,428 | (G)6→5 | coding (110/2319 nt) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,849,433 | G→A | T235M (ACG→ATG) | uhpB ← | sensory histidine kinase UhpB |
| RA | 3,852,208 | C→T | A193T (GCC→ACC) | ilvB ← | acetohydroxy acid synthase I subunit IlvB |
| RA | 3,854,090 | G→A | G57S (GGT→AGT) | emrD → | multidrug efflux pump EmrD |
| RA | 3,856,753 | (T)5→6 | coding (339/450 nt) | yidI → | putative inner membrane protein |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,864,868 | T→C | Y469C (TAT→TGT) | yidE ← | putative transport protein YidE |
| RA | 3,885,636 | G→A | P187P (CCG→CCA) | yidC → | membrane protein insertase YidC |
| RA | 3,890,443 | G→A | G70S (GGC→AGC) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 3,898,816 | A→C | V193G (GTC→GGC) | yieK ← | putative glucosamine‑6‑phosphate deaminase YieK |
| RA | 3,922,549 | (C)5→4 | intergenic (‑109/+508) | atpI ← / ← rsmG | ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase |
| RA | 3,925,336 | C→G | D100H (GAT→CAT) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,949,304 | A→G | G222G (GGT→GGC) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,953,356 | C→T | G291G (GGC→GGT) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,956,738 | A→G | T470A (ACC→GCC) | ilvA → | threonine deaminase |
| RA | 3,976,956 | A→G | T227A (ACG→GCG) | wzxE → | lipid III flippase |
| RA | 3,999,720 | T→C | F580L (TTC→CTC) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 4,007,246 | C→T | G461G (GGC→GGT) | recQ → | ATP‑dependent DNA helicase RecQ |
| RA | 4,010,309 | A→G | N37S (AAC→AGC) | yigL → | phosphosugar phosphatase YigL |
| RA | 4,032,000 | A→G | E280E (GAA→GAG) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,053,014 | A→G | M324V (ATG→GTG) | hemN → | coproporphyrinogen III dehydrogenase |
| RA | 4,062,831 | A→G | A195A (GCA→GCG) | yihN → | putative transporter YihN |
| RA | 4,104,208 | A→G | R256R (CGT→CGC) | cpxA ← | sensory histidine kinase CpxA |
| RA | 4,126,222 | A→G | L197L (TTG→CTG) | priA ← | primosome factor N' |
| RA | 4,151,270 | A→G | V610A (GTA→GCA) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,156,584 | A→G | Q191R (CAA→CGA) | argB → | acetylglutamate kinase |
| RA | 4,181,903 | T→C | I220T (ATC→ACC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,233,858 | A→G | D34G (GAC→GGC) | pgi → | glucose‑6‑phosphate isomerase |
| RA | 4,241,484 | T→C | K257K (AAA→AAG) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,267,558 | C→T | P149S (CCC→TCC) | tyrB → | tyrosine aminotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,302,825 | A→G | V85A (GTG→GCG) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| JC JC | 4,306,431 | IS1 (+) +9 bp | coding (159‑167/1986 nt) | yjcS ← | alkyl sulfatase |
| RA | 4,429,416 | C→T | A161V (GCA→GTA) | fklB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase FklB |
| RA | 4,441,848 | T→C | Q110R (CAG→CGG) | msrA ← | methionine sulfoxide reductase A |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,451,045 | A→G | intergenic (+127/‑13) | ytfQ → / → ytfR | galactofuranose ABC transporter periplasmic binding protein/galactofuranose ABC transporter putative ATP binding subunit |
| RA | 4,454,129 | A→G | T183A (ACC→GCC) | yjfF → | galactofuranose ABC transporter putative membrane subunit YjtF |
| RA | 4,468,257 | G→A | S211S (TCG→TCA) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,474,275 | (C)6→7 | coding (152/594 nt) | bdcR → | putative transcriptional regulator BdcR |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,493,414 | A→G | G331G (GGT→GGC) | idnD ← | L‑idonate 5‑dehydrogenase |
| RA | 4,504,246 | A→G | R63R (AGA→AGG) | yjhB → | putative sialic acid transporter |
| RA | 4,520,902 | A→G | G373G (GGT→GGC) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,528,706 | A→G | V71A (GTG→GCG) | sgcQ ← | KpLE2 phage‑like element; putative nucleoside triphosphatase |
| RA | 4,565,988 | A→G | L420S (TTG→TCG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| RA | 4,578,548 | G→A | Q264* (CAG→TAG) | mcrB ← | 5‑methylcytosine‑specific restriction enzyme subunit McrB |
| RA | 4,586,655 | A→G | L36P (CTG→CCG) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,590,443 | T→C | A279A (GCA→GCG) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,593,296 | A→G | N547S (AAC→AGC) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,604,288 | T→C | S43S (AGT→AGC) | bglJ → | DNA‑binding transcriptional regulator BglJ |
| JC | 4,606,215 | (G)8→11 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,329 | (G)8→6 | noncoding (72‑73/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,611,965 | T→C | G190G (GGT→GGC) | osmY → | periplasmic chaperone OsmY |
| RA | 4,629,935 | T→C | E196E (GAA→GAG) | ettA ← | energy‑dependent translational throttle protein EttA |
| RA | 4,630,384 | T→C | T47A (ACC→GCC) | ettA ← | energy‑dependent translational throttle protein EttA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 270640–271482 | 271482 | 1–843 | 40 [35] | [33] 40 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 731427–731470 | 731586–731521 | 52–160 | 38 [35] | [32] 37 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 732702–732959 | 734610–734476 | 1518–1909 | 37 [35] | [35] 37 | [rhsC]–[ybfO] | [rhsC],ybfB,[ybfO] |
| * | * | ÷ | NC_000913 | 1269855–1269921 | 1270363–1270091 | 171–509 | 36 [35] | [35] 36 | rdlB–ldrC | rdlB,ldrC |
| * | * | ÷ | NC_000913 | 1286784 | 1286915–1286885 | 102–132 | 37 [35] | [35] 36 | ychS | putative uncharacterized protein YchS |
| * | * | ÷ | NC_000913 | 3423762–3424234 | 3424525–3424238 | 5–764 | 36 [35] | [29] 37 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 11 (0.070) | 145 (1.110) | 73/244 | 0.2 | 91.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 18 (0.140) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.070) | 83 (0.640) | 52/244 | 0.7 | 85.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 18 (0.140) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 204 (1.420) | 97/268 | 0.0 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 305 (2.070) | 338 (2.310) | 99/274 | 0.0 | 68.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 8 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 194 (1.310) | 90/276 | 0.1 | 94.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 11 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||