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 | 46,840 | C→T | A345V (GCC→GTC) | yaaU → | putative transporter YaaU |
| RA | 63,556 | T→C | Y742C (TAC→TGC) | polB ← | DNA polymerase II |
| RA | 78,721 | (G)5→7 | coding (1101/1179 nt) | setA → | sugar exporter SetA |
| RA | 93,241 | A→G | T26A (ACA→GCA) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 103,198 | T→C | V15A (GTT→GCT) | ftsQ → | cell division protein FtsQ |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/SecA translation regulator |
| RA | 136,457 | (T)8→7 | coding (8/867 nt) | speE ← | spermidine synthase |
| RA | 152,110 | A→G | V41A (GTA→GCA) | yadL ← | putative fimbrial protein YadL |
| RA | 178,095 | (G)5→6 | coding (368/801 nt) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 181,996 | T→C | G371G (GGT→GGC) | degP → | periplasmic serine endoprotease DegP |
| RA | 216,269 | C→A | A245A (GCG→GCT) | yaeF ← | peptidase C92 family protein |
| RA | 235,772 | A→G | G77G (GGT→GGC) | rnhA ← | ribonuclease HI |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 281,050 | (G)5→6 | coding (934/1155 nt) | yagA ← | CP4‑6 prophage; integrase core domain‑containing protein YagA |
| RA | 317,251 | T→C | intergenic (‑115/+475) | ykgA ← / ← rclC | putative DNA‑binding transcriptional regulator YkgA/reactive chlorine species resistance protein C |
| RA | 333,796 | A→G | V213A (GTG→GCG) | yahB ← | putative LysR‑type DNA‑binding transcriptional regulator YahB |
| RA | 356,058 | A→G | L379L (TTA→TTG) | codB → | cytosine transporter |
| RA | 359,829 | A→G | E114G (GAG→GGG) | cynS → | cyanase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 434,513 | A→G | I353M (ATA→ATG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 477,430 | T→C | E396E (GAA→GAG) | pdeB ← | c‑di‑GMP phosphodiesterase PdeB |
| RA | 482,784 | A→G | R540R (CGT→CGC) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 493,451 | A→G | T454A (ACC→GCC) | dnaX → | DNA polymerase III subunit tau |
| RA | 505,107 | G→A | G65D (GGT→GAT) | ushA → | 5'‑nucleotidase/UDP‑sugar hydrolase |
| RA | 510,729 | G→A | S217S (AGC→AGT) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 548,964 | Δ1 bp | coding (608/1260 nt) | ylbE → | DUF1116 domain‑containing protein YlbE |
| RA | 555,650 | A→G | D347G (GAC→GGC) | cysS → | cysteine‑‑tRNA ligase |
| RA | 591,428 | C→A | G584V (GGC→GTC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 600,439 | A→G | T576A (ACG→GCG) | cusA → | copper/silver export system RND permease |
| RA | 605,132 | A→G | V98A (GTT→GCT) | nfsB ← | NAD(P)H nitroreductase NfsB |
| RA | 655,867 | A→G | G34G (GGT→GGC) | dcuC ← | anaerobic C4‑dicarboxylate transporter DcuC |
| RA | 735,986 | (A)6→7 | coding (337/570 nt) | ybfC → | uncharacterized protein YbfC |
| RA | 737,376 | A→G | pseudogene (477/1062 nt) | ybfL → | putative transposase YbfL |
| RA | 791,005 | G→A | H9Y (CAT→TAT) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 805,840 | G→A | intergenic (+76/+158) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 805,853 | Δ1 bp | intergenic (+89/+145) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 805,855 | T→C | intergenic (+91/+143) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 805,863 | A→G | intergenic (+99/+135) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 805,872 | A→G | intergenic (+108/+126) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 805,876 | T→A | intergenic (+112/+122) | ybhJ → / ← ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| RA | 817,144 | A→G | D34G (GAT→GGT) | moaA → | GTP 3',8'‑cyclase |
| RA | 819,624 | C→T | A110A (GCC→GCT) | moaE → | molybdopterin synthase catalytic subunit |
| RA | 845,350 | (T)8→9 | coding (131/2226 nt) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 854,750 | A→G | I368M (ATA→ATG) | ybiR → | putative transporter YbiR |
| RA | 859,698 | T→C | S111G (AGT→GGT) | ybiV ← | sugar phosphatase |
| RA | 886,543 | A→G | V266A (GTT→GCT) | ybjJ ← | inner membrane protein YbjJ |
| RA | 888,832 | A→G | F330L (TTC→CTC) | ybjL ← | putative transport protein YbjL |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 913,631 | C→T | V62I (GTT→ATT) | hcp ← | protein S‑nitrosylase |
| RA | 924,084 | T→C | L274P (CTG→CCG) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| JC | 925,899 | (G)7→10 | noncoding (73/88 nt) | serW ← | tRNA‑Ser |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 989,044 | (G)6→7 | intergenic (‑59/+110) | asnS ← / ← pncB | asparagine‑‑tRNA ligase/nicotinate phosphoribosyltransferase |
| RA | 993,073 | C→T | R818C (CGT→TGT) | pepN → | aminopeptidase N |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,011,593 | (A)7→8 | coding (1630/1908 nt) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,013,756 | (A)6→7 | coding (498/1641 nt) | pqiB → | intermembrane transport protein PqiB |
| RA | 1,015,783 | A→G | G23G (GGA→GGG) | rmf → | ribosome modulation factor |
| RA | 1,019,827 | T→C | Y76C (TAC→TGC) | ompA ← | outer membrane porin A |
| RA | 1,048,289 | A→G | L135L (TTG→CTG) | gfcC ← | capsule biosynthesis GfcC family protein |
| RA | 1,093,865 | (G)5→6 | coding (990/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,103,670 | C→T | intergenic (‑474/‑281) | csgD ← / → csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| RA | 1,131,261 | A→G | T82A (ACC→GCC) | flgB → | flagellar basal‑body rod protein FlgB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,154,463 | A→G | M118V (ATG→GTG) | mltG → | endolytic murein transglycosylase |
| RA | 1,159,369 | T→C | Q728R (CAA→CGA) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,167,348 | A→G | S422G (AGT→GGT) | ndh → | NADH:quinone oxidoreductase II |
| RA | 1,178,196 | A→G | M293V (ATG→GTG) | lolE → | lipoprotein release complex ‑ inner membrane subunit |
| 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 | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,231,808 | A→G | D208G (GAT→GGT) | umuC → | DNA polymerase V catalytic protein |
| RA | 1,240,112 | G→A | intergenic (+163/‑148) | dadX → / → ymgM | alanine racemase 2/protein YmgM |
| RA | 1,240,528 | C→T | G515D (GGC→GAC) | cvrA ← | putative K(+):H(+) antiporter |
| RA | 1,286,999 | C→T | intergenic (+15/+67) | ychS → / ← rttR | putative uncharacterized protein YchS/small RNA RttR |
| RA | 1,289,658 | T→C | S138S (AGT→AGC) | rssA → | putative patatin‑like phospholipase RssA |
| RA | 1,302,129 | T→C | R316R (CGT→CGC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,314,053 | A→G | T12A (ACA→GCA) | ompW → | outer membrane protein W |
| RA | 1,314,648 | A→G | Y210C (TAT→TGT) | ompW → | outer membrane protein W |
| RA | 1,324,113 | (T)7→6 | coding (16/621 nt) | yciO → | putative RNA‑binding protein YciO |
| RA | 1,352,655 | A→G | L325P (CTG→CCG) | sapD ← | putrescine ABC exporter ATP binding protein SapD |
| RA | 1,352,747 | Δ1 bp | coding (882/993 nt) | sapD ← | putrescine ABC exporter ATP binding protein SapD |
| RA | 1,373,237 | (T)6→5 | coding (16/882 nt) | ycjO → | putative ABC transporter membrane subunit YcjO |
| RA | 1,392,761 | (A)8→9 | coding (771/900 nt) | pgrR → | DNA‑binding transcriptional repressor PgrR |
| RA | 1,419,721 | (G)7→6 | intergenic (‑265/+44) | ydaG ← / ← racR | Rac prophage; uncharacterized protein YdaG/Rac prophage; DNA‑binding transcriptional repressor RacR |
| RA | 1,426,089 | T→C | intergenic (+109/‑365) | ydaY → / → ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← ydbK | small regulatory RNA MicC/putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,437,788 | A→G | G999G (GGT→GGC) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,495,485 | A→G | E66E (GAA→GAG) | ydcJ → | DUF1338 domain‑containing protein YdcJ |
| RA | 1,499,118 | T→C | L61L (TTG→CTG) | rimL → | ribosomal‑protein‑L12‑serine acetyltransferase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,544,042 | (T)5→4 | coding (19/1389 nt) | narU ← | nitrate/nitrite transporter NarU |
| RA | 1,550,878 | A→G | I140V (ATT→GTT) | fdnH → | formate dehydrogenase N subunit beta |
| RA | 1,555,655 | (T)7→8 | coding (15/1698 nt) | maeA ← | malate dehydrogenase, NAD‑requiring |
| RA | 1,577,059 | A→G | T187T (ACT→ACC) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,587,142 | T→C | D198G (GAC→GGC) | ydeQ ← | putative fimbrial adhesin protein YdeQ |
| RA | 1,597,313 | (C)7→6 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,603,815 | T→C | V266A (GTA→GCA) | lsrC → | Autoinducer‑2 ABC transporter membrane subunit LsrC |
| RA | 1,607,262 | (A)6→7 | coding (264/291 nt) | lsrG → | (4S)‑4‑hydroxy‑5‑phosphonooxypentane‑2,3‑dione isomerase |
| RA | 1,655,044 | T→C | D33G (GAT→GGT) | rspA ← | mandelate racemase/muconate lactonizing enzyme family protein RspA |
| RA | 1,675,608 | (C)5→6 | coding (753/1389 nt) | pntB ← | pyridine nucleotide transhydrogenase subunit beta |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,695,724 | G→A | A116A (GCC→GCT) | uidA ← | beta‑glucuronidase |
| RA | 1,699,694 | T→C | F114L (TTC→CTC) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,704,167 | G→A | P48S (CCA→TCA) | ydgJ ← | putative oxidoreductase YdgJ |
| RA | 1,709,945 | A→G | A268A (GCA→GCG) | rsxD → | SoxR [2Fe‑2S] reducing system protein RsxD |
| RA | 1,712,518 | (C)6→7 | intergenic (+360/‑251) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,749,745 | A→G | C202R (TGT→CGT) | ydhU ← | putative cytochrome YdhU |
| RA | 1,753,415 | Δ1 bp | coding (416/2103 nt) | ydhV ← | putative oxidoreductase |
| RA | 1,754,383 | G→A | A32V (GCC→GTC) | ydhY ← | putative 4Fe‑4S ferredoxin‑type protein |
| RA | 1,764,003 | G→A | R3C (CGT→TGT) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,806,659 | T→C | V97A (GTG→GCG) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,812,736 | A→G | L133L (TTG→CTG) | ydjO ← | protein YdjO |
| RA | 1,818,550 | (C)7→8 | intergenic (‑50/+55) | chbF ← / ← chbR | monoacetylchitobiose‑6‑phosphate hydrolase/DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,853,893 | A→G | F29F (TTT→TTC) | ydjE ← | putative transporter YdjE |
| RA | 1,860,891 | C→T | V148I (GTT→ATT) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,864,670 | C→T | T274M (ACG→ATG) | yeaD → | putative aldose 1‑epimerase YeaD |
| RA | 1,865,169 | (C)6→7 | coding (468/855 nt) | yeaE ← | methylglyoxal reductase YeaE |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,877,866 | A→G | Q51R (CAG→CGG) | dgcP → | diguanylate cyclase DgcP |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,882,756 | T→C | V282A (GTC→GCC) | dmlA → | D‑malate/3‑isopropylmalate dehydrogenase (decarboxylating) |
| RA | 1,920,963 | T→C | C247C (TGT→TGC) | rsmF → | 16S rRNA m(5)C1407 methyltransferase |
| RA | 1,934,179 | A→G | H142H (CAT→CAC) | edd ← | phosphogluconate dehydratase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,046,898 | T→C | V654A (GTG→GCG) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,051,982 | T→C | F2349L (TTT→CTT) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,071,189 | T→C | pseudogene (404/426 nt) | yeeP → | CP4‑44 prophage; putative GTP‑binding protein |
| RA | 2,072,464 | A→G | K309R (AAG→AGG) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,073,366 | A→G | T610A (ACC→GCC) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,081,698 | T→C | T284A (ACG→GCG) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase DacD |
| RA | 2,091,712 | Δ1 bp | coding (616/1305 nt) | hisD → | histidinal/histidinol dehydrogenase |
| RA | 2,125,570 | T→C | K59K (AAA→AAG) | wcaI ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,132,104 | A→G | V151A (GTG→GCG) | wcaB ← | putative colanic acid biosynthesis acyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,185,726 | G→A | A24V (GCG→GTG) | rcnR ← | DNA‑binding transcriptional repressor RcnR |
| RA | 2,193,357 | A→G | V271A (GTG→GCG) | mrp ← | P‑loop NTPase family protein |
| RA | 2,232,893 | T→C | F6L (TTC→CTC) | sanA → | DUF218 domain‑containing protein SanA |
| RA | 2,240,754 | (C)5→4 | coding (915/1041 nt) | galS ← | DNA‑binding transcriptional dual regulator GalS |
| RA | 2,247,128 | G→A | L469L (CTG→TTG) | lysP ← | lysine:H(+) symporter |
| RA | 2,270,127 | T→C | L50P (CTG→CCG) | mepS → | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase |
| RA | 2,295,852 | G→A | R157C (CGT→TGT) | ccmC ← | heme trafficking system membrane protein CcmC |
| RA | 2,336,634 | (T)7→6 | coding (11/1689 nt) | yfaA ← | DUF2138 domain‑containing protein YfaA |
| RA | 2,381,001 | A→G | R9R (CGT→CGC) | elaB ← | tail anchored inner membrane protein |
| RA | 2,430,323 | (A)7→8 | coding (441/489 nt) | cvpA ← | colicin V production protein |
| RA | 2,442,697 | T→C | Y312H (TAT→CAT) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,455,256 | T→C | T131A (ACC→GCC) | yfcV ← | putative fimbrial protein YfcV |
| RA | 2,457,177 | T→C | G661G (GGA→GGG) | fadJ ← | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| 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 | 2,484,057 | T→C | S101S (AGT→AGC) | evgA → | DNA‑binding transcriptional activator EvgA |
| RA | 2,496,075 | G→A | G144E (GGA→GAA) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,497,153 | G→A | D381D (GAC→GAT) | alaC ← | glutamate‑‑pyruvate aminotransferase AlaC |
| RA | 2,500,410 | T→C | F10L (TTC→CTC) | ypdB → | DNA‑binding transcriptional activator YpdB |
| RA | 2,507,334 | T→C | L187L (TTA→TTG) | fryC ← | putative PTS enzyme IIC component FryC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,543,052 | A→G | R159R (CGT→CGC) | cysP ← | thiosulfate/sulfate ABC transporter periplasmic binding protein CysP |
| RA | 2,579,515 | C→T | H284Y (CAC→TAC) | talA → | transaldolase A |
| RA | 2,598,045 | C→T | G274D (GGC→GAC) | bamC ← | outer membrane protein assembly factor BamC |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,604,172 | T→C | I109T (ATC→ACC) | hyfC → | hydrogenase 4 component C |
| RA | 2,620,850 | T→C | H8R (CAC→CGC) | upp ← | uracil phosphoribosyltransferase |
| RA | 2,632,973 | A→G | G366G (GGT→GGC) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,663,078 | A→G | R82R (CGT→CGC) | trmJ ← | tRNA Cm32/Um32 methyltransferase |
| RA | 2,690,350 | C→A | R250L (CGC→CTC) | glrK ← | sensory histidine kinase GlrK |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,737,713 | (G)6→7 | intergenic (+67/‑32) | pheL → / → pheA | phe operon leader peptide/fused chorismate mutase/prephenate dehydratase |
| RA | 2,738,236 | T→C | G164G (GGT→GGC) | pheA → | fused chorismate mutase/prephenate dehydratase |
| RA | 2,770,922 | G→A | G81D (GGT→GAT) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,938 | T→C | Y86Y (TAT→TAC) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,941 | G→C | L87L (CTG→CTC) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,944 | A→G | V88V (GTA→GTG) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,951 | G→C | E91Q (GAG→CAG) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,956 | G→A | E92E (GAG→GAA) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,770,971 | G→A | P97P (CCG→CCA) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,771,040 | G→C | T120T (ACG→ACC) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,771,055 | C→T | F125F (TTC→TTT) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,771,058 | A→G | E126E (GAA→GAG) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,771,061 | 2 bp→CG | coding (381‑382/444 nt) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,776,420 | T→C | V12A (GTA→GCA) | yfjY → | CP4‑57 prophage; RadC‑like JAB domain‑containing protein YfjY |
| RA | 2,807,382 | T→C | V84A (GTG→GCG) | proX → | glycine betaine ABC transporter periplasmic binding protein ProX |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,852,654 | C→T | C173C (TGC→TGT) | hypD → | Fe‑(CN)2CO cofactor assembly scaffold protein HypD |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,872,552 | T→C | D90G (GAC→GGC) | ftsB ← | cell division protein FtsB |
| RA | 2,925,689 | G→A | T114T (ACG→ACA) | queF → | 7‑cyano‑7‑deazaguanine reductase |
| RA | 2,943,707 | T→C | V124A (GTC→GCC) | csdA → | cysteine sulfinate desulfinase |
| RA | 2,947,343 | (A)8→7 | intergenic (‑165/‑44) | mltA ← / → metZ | membrane‑bound lytic murein transglycosylase A/tRNA‑Met |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,965,754 | A→G | V95A (GTC→GCC) | lgt ← | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase |
| RA | 2,966,716 | T→C | E573E (GAA→GAG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| JC | 3,003,479 | (G)6→9 | coding (866/879 nt) | xdhB → | putative xanthine dehydrogenase FAD‑binding subunit XdhB |
| RA | 3,009,850 | A→T | I363F (ATC→TTC) | ygeY → | putative peptidase YgeY |
| RA | 3,051,344 | T→C | D325G (GAC→GGC) | ubiI ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,060,561 | A→G | H270R (CAC→CGC) | argP → | DNA‑binding transcriptional dual regulator ArgP |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,069,712 | C→T | V32V (GTG→GTA) | mscS ← | small conductance mechanosensitive channel MscS |
| RA | 3,082,192 | T→C | Y94H (TAT→CAT) | loiP → | metalloprotease LoiP |
| RA | 3,108,382 | G→A | R258R (CGC→CGT) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,123,593 | A→G | N71N (AAT→AAC) | glcB ← | malate synthase G |
| RA | 3,158,920 | A→G | intergenic (+36/+7) | yqhH → / ← ygiQ | lipoprotein YqhH/radical SAM superfamily protein YgiQ |
| RA | 3,160,127 | A→G | P340P (CCT→CCC) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,191,379 | A→G | T250A (ACG→GCG) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,198,044 | A→G | V533A (GTG→GCG) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,229,583 | T→C | G232G (GGT→GGC) | ygjK → | glycoside hydrolase |
| RA | 3,263,316 | T→C | A115A (GCA→GCG) | tdcD ← | propionate kinase |
| RA | 3,270,488 | (C)7→8 | noncoding (105/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,290,126 | A→G | D438G (GAC→GGC) | yraJ → | putative fimbrial usher protein YraJ |
| RA | 3,300,074 | Δ1 bp | coding (109/303 nt) | yhbQ → | DNA damage response nuclease YhbQ |
| JC | 3,337,101 | (C)6→9 | coding (156/294 nt) | mlaB ← | intermembrane phospholipid transport system protein MlaB |
| RA | 3,347,536 | T→C | V141A (GTT→GCT) | rapZ → | RNase adaptor protein |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,362,424 | T→C | F105L (TTC→CTC) | yhcA → | putative fimbrial chaperone YhcA |
| RA | 3,375,895 | (G)6→5 | coding (1027/1368 nt) | dcuD → | putative transporter DcuD |
| RA | 3,386,282 | T→C | E636G (GAA→GGA) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,398,446 | G→A | L144F (CTC→TTC) | mreD ← | cell shape determining protein MreD |
| RA | 3,407,296 | Δ1 bp | intergenic (+30/‑79) | accC → / → yhdT | biotin carboxylase/DUF997 domain‑containing protein YhdT |
| RA | 3,420,535 | T→C | I134I (ATT→ATC) | yhdX → | putative ABC transporter membrane subunit YhdX |
| RA | 3,457,425 | T→C | V350A (GTT→GCT) | gspD → | Type II secretion system protein GspD |
| RA | 3,462,844 | (G)6→7 | coding (501/588 nt) | gspJ → | Type II secretion system protein GspJ |
| RA | 3,463,197 | A→G | T92A (ACA→GCA) | gspK → | Type II secretion system protein GspK |
| JC JC | 3,470,056 | IS1 (–) +8 bp | intergenic (‑203/+82) | chiA ← / ← tufA | endochitinase/translation elongation factor Tu 1 |
| RA | 3,518,153 | C→T | G112S (GGC→AGC) | aroB ← | 3‑dehydroquinate synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,564,565 | T→C | T673A (ACG→GCG) | glgP ← | glycogen phosphorylase |
| RA | 3,573,754 | C→T | intergenic (‑252/+21) | glgB ← / ← asd | 1,4‑alpha‑glucan branching enzyme/aspartate‑semialdehyde dehydrogenase |
| RA | 3,576,313 | A→G | V250A (GTG→GCG) | gntU ← | low‑affinity gluconate transporter |
| MC JC | 3,581,940 | Δ1,488 bp | IS1‑mediated | [yhhZ]–[yrhA] | [yhhZ], [yrhA] |
| RA | 3,606,118 | C→T | T123M (ACG→ATG) | yhhN → | conserved inner membrane enzyme YhhN |
| RA | 3,629,501 | G→A | A13V (GCG→GTG) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,664,399 | A→G | L74L (TTA→CTA) | gadW ← | DNA‑binding transcriptional dual regulator GadW |
| RA | 3,740,385 | T→C | G227G (GGT→GGC) | avtA → | valine‑‑pyruvate aminotransferase |
| RA | 3,750,873 | A→G | intergenic (+92/+255) | sgbE → / ← yiaT | L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT |
| RA | 3,753,644 | G→A | S152S (AGC→AGT) | yiaV ← | putative membrane fusion protein |
| RA | 3,756,083 | A→G | G143G (GGT→GGC) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,783,799 | A→G | A110A (GCT→GCC) | secB ← | SecB chaperone |
| RA | 3,807,692 | A→G | L136P (CTT→CCT) | waaQ ← | lipopolysaccharide core heptosyltransferase 3 |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,854,055 | T→C | V45A (GTG→GCG) | emrD → | multidrug efflux pump EmrD |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,863,379 | T→C | L75L (TTA→TTG) | glvC ← | putative PTS enzyme II component GlvC |
| RA | 3,881,409 | T→C | I305V (ATC→GTC) | dnaN ← | beta sliding clamp |
| RA | 3,894,592 | G→A | A238T (GCC→ACC) | yieE → | putative phosphopantetheinyl transferase |
| RA | 3,915,903 | T→C | I24V (ATC→GTC) | atpC ← | ATP synthase F1 complex subunit epsilon |
| RA | 3,930,842 | A→G | G84G (GGT→GGC) | ravA ← | regulatory ATPase RavA |
| RA | 3,935,976 | T→C | L230P (CTG→CCG) | rbsC → | ribose ABC transporter membrane subunit |
| RA | 3,937,409 | C→T | A39V (GCA→GTA) | rbsK → | ribokinase |
| RA | 3,944,122 | T→C | noncoding (419/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,945,556 | A→G | noncoding (1853/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,955,349 | C→T | L7L (CTG→TTG) | ilvA → | threonine deaminase |
| RA | 3,972,840 | A→G | T107A (ACA→GCA) | rffG → | dTDP‑glucose 4,6‑dehydratase 2 |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,994,961 | G→T | G67V (GGC→GTC) | dapF → | diaminopimelate epimerase |
| RA | 4,018,153 | A→G | Y274C (TAC→TGC) | rmuC → | putative recombination limiting protein RmuC |
| RA | 4,023,436 | G→A | R234H (CGC→CAC) | tatC → | twin arginine protein translocation system ‑ TatC protein |
| RA | 4,043,282 | T→C | F290L (TTC→CTC) | srkA → | stress response kinase A |
| RA | 4,068,440 | G→A | G279G (GGC→GGT) | yihQ ← | sulfoquinovosidase |
| RA | 4,069,512 | T→C | H297R (CAC→CGC) | yihR ← | putative aldose 1‑epimerase YihR |
| RA | 4,105,864 | C→T | V15V (GTC→GTT) | cpxP → | periplasmic protein CpxP |
| RA | 4,155,941 | C→T | A314V (GCG→GTG) | argC → | N‑acetylglutamylphosphate reductase |
| RA | 4,165,497 | G→A | V24M (GTG→ATG) | murI → | glutamate racemase |
| RA | 4,209,713 | G→A | intergenic (+25/‑61) | rrsE → / → gltV | 16S ribosomal RNA/tRNA‑Glu |
| RA | 4,232,375 | T→C | T287A (ACG→GCG) | lysC ← | aspartate kinase III |
| RA | 4,236,508 | A→G | T83A (ACT→GCT) | yjbF → | lipoprotein YjbF |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,351,784 | T→C | intergenic (‑122/‑59) | dcuS ← / → yjdI | sensory histidine kinase DcuS/PF06902 family protein YjdI |
| RA | 4,358,040 | T→C | H193R (CAC→CGC) | cadA ← | lysine decarboxylase 1 |
| RA | 4,401,719 | A→G | I350V (ATA→GTA) | hflX → | ribosome rescue factor HflX |
| RA | 4,419,193 | Δ1 bp | coding (433/1065 nt) | ulaG ← | L‑ascorbate‑6‑phosphate lactonase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,448,792 | T→C | V34A (GTG→GCG) | chpB → | endoribonuclease toxin ChpB |
| RA | 4,449,073 | (A)7→6 | intergenic (+31/+49) | chpB → / ← ppa | endoribonuclease toxin ChpB/inorganic pyrophosphatase |
| RA | 4,509,750 | A→G | pseudogene (272/315 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,513,105 | G→A | A102V (GCG→GTG) | fecC ← | ferric citrate ABC transporter membrane subunit FecC |
| RA | 4,518,721 | A→G | G65G (GGA→GGG) | insA‑7 → | KpLE2 phage‑like element; IS1 repressor protein InsA |
| RA | 4,544,301 | A→G | intergenic (+34/‑3) | fimI → / → fimC | putative fimbrial protein FimI/type 1 fimbriae periplasmic chaperone |
| RA | 4,547,436 | A→G | T781A (ACT→GCT) | fimD → | type I fimbriae usher protein |
| RA | 4,567,286 | (A)5→4 | intergenic (‑40/+1) | yjiN ← / ← mdtM | DUF445 domain‑containing protein YjiN/multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 4,569,491 | A→G | pseudogene (494/921 nt) | rpnD → | truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,571,048 | C→T | G176D (GGC→GAC) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,606,215 | (G)8→10 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,607,596 | C→T | A35A (GCG→GCA) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase |
| RA | 4,637,666 | T→C | V324A (GTT→GCT) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 734881–734938 | 734977–734943 | 6–97 | 7 [6] | [5] 7 | ybfO | conserved protein, rhs‑like YbfO |
| * | * | ÷ | NC_000913 | 1196292 | 1211419 | 15128 | 7 [5] | [6] 8 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 1633325–1633923 | 1634911–1634647 | 725–1587 | 7 [5] | [6] 7 | pinQ–[ydfN] | pinQ,tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 2304661–2304783 | 2304922–2304802 | 20–262 | 7 [6] | [6] 7 | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| * | * | ÷ | NC_000913 | 2770984–2770997 | 2771025 | 29–42 | 10 [5] | [5] 8 | yfjS | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| * | * | ÷ | NC_000913 | 3423787–3424234 | 3424518–3424239 | 6–732 | 7 [6] | [2] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619340–3622297 | 3622416–3622379 | 83–3077 | 7 [6] | [6] 7 | rhsB | rhs element protein RhsB |
| * | * | ÷ | NC_000913 | 4168394–4168477 | 4171635–4168572 | 96–3242 | 7 [6] | [3] 7 | [gltT]–rrlB | [gltT],rrlB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 53 (1.250) | 38/268 | 0.1 | 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 = | 79 (1.800) | 87 (2.000) | 53/274 | 0.0 | 68.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 56 (1.280) | 43/276 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 41 (0.940) | 12 (0.290) | 9/258 | 2.1 | 20.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 57 (1.390) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||