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 | 108,585 | C→T | R103C (CGT→TGT) | secA → | protein translocation ATPase |
| RA | 134,256 | G→T | intergenic (+44/‑132) | acnB → / → yacL | AcnB/PF06062 family protein YacL |
| RA | 156,068 | A→G | V45A (GTA→GCA) | yadV ← | putative fimbrial chaperone YadV |
| RA | 157,043 | G→A | intergenic (‑160/+210) | yadN ← / ← folK | putative fimbrial protein YadN/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase |
| JC JC | 167,915 | IS2 (–) +5 bp | coding (432‑436/2244 nt) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 287,356 | C→T | L190L (CTG→TTG) | yagH → | putative xylosidase/arabinosidase |
| RA | 289,091 | A→G | L24L (CTT→CTC) | xynR ← | DNA‑binding transcriptional repressor XynR |
| RA | 306,212 | 2 bp→AA | coding (605‑606/1644 nt) | ecpD ← | fimbrial adhesin EcpD |
| RA | 322,064 | C→T | L153L (CTG→TTG) | ykgE → | putative lactate utilization oxidoreductase YkgE |
| RA | 338,135 | C→T | A453V (GCG→GTG) | yahF → | putative acyl‑CoA synthetase YahF |
| JC JC | 362,204 | IS1 (–) +9 bp | coding (968‑976/1254 nt) | lacY ← | lactose permease |
| JC JC | 432,120 | IS1 (+) +9 bp | intergenic (‑107/+184) | tsx ← / ← yajI | nucleoside‑specific channel‑forming protein Tsx/putative lipoprotein YajI |
| RA | 458,188 | G→A | D255N (GAT→AAT) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 459,432 | C→T | S182F (TCT→TTT) | lon → | Lon protease |
| RA | 459,572 | T→G | Y229D (TAT→GAT) | lon → | Lon protease |
| RA | 462,394 | C→A | L160L (CTC→CTA) | ppiD → | periplasmic folding chaperone |
| RA | 534,124 | G→C | G70A (GGC→GCC) | gcl → | glyoxylate carboligase |
| RA | 543,263 | 2 bp→GT | coding (783‑784/786 nt) | allE ← | (S)‑ureidoglycine aminohydrolase |
| JC JC | 562,453 | IS2 (–) +5 bp | coding (118‑122/984 nt) | sfmH → | putative fimbrial adhesin protein SfmH |
| MC JC | 575,786 | Δ3,398 bp | IS5‑mediated | [nmpC]–borD | [nmpC], essD, rrrD, rzpD, rzoD, borD |
| RA | 628,569 | A→G | N7D (AAT→GAT) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| JC JC | 637,849 | IS1 (+) +9 bp | coding (717‑725/747 nt) | dsbG ← | protein sulfenic acid reductase and chaperone DsbG |
| JC JC | 646,571 | IS5 (+) +4 bp | coding (7‑10/1464 nt) | citT ← | citrate:succinate antiporter |
| RA | 659,517 | G→A | L234L (CTG→TTG) | lipA ← | lipoyl synthase |
| RA | 659,527 | G→T | T230T (ACC→ACA) | lipA ← | lipoyl synthase |
| MC JC | 696,507 | Δ112 bp | glnV | glnV | |
| RA | 727,761 | C→T | E324E (GAG→GAA) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 732,828 | T→C | G1082G (GGT→GGC) | rhsC → | rhs element protein RhsC |
| JC JC | 735,613 | IS5 (+) +4 bp | intergenic (+1511/‑34) | ybfB → / → ybfC | uncharacterized protein YbfB/uncharacterized protein YbfC |
| RA | 740,655 | G→A | W383* (TGG→TGA) | phr → | deoxyribodipyrimidine photolyase |
| JC | 755,780 | Δ7 bp | coding (221‑227/348 nt) | sdhD → | succinate:quinone oxidoreductase, membrane protein SdhD |
| RA | 758,593 | T→C | intergenic (+188/‑113) | sdhB → / → sucA | succinate:quinone oxidoreductase, iron‑sulfur cluster binding protein/subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 768,617 | G→A | E214K (GAG→AAG) | mngB → | alpha‑mannosidase |
| RA | 789,853 | C→A | V43F (GTT→TTT) | galK ← | galactokinase |
| RA | 790,086 | C→T | G315D (GGT→GAT) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 854,975 | G→A | S257F (TCT→TTT) | ldtB ← | L,D‑transpeptidase LdtB |
| RA | 856,434 | C→T | P158S (CCT→TCT) | ybiT → | putative ATP‑binding protein YbiT |
| RA | 857,041 | C→A | T360K (ACG→AAG) | ybiT → | putative ATP‑binding protein YbiT |
| RA | 873,398 | Δ1 bp | coding (420/2349 nt) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 973,577 | C→T | S14F (TCC→TTC) | cmoM → | tRNA cmo(5)U34 methyltransferase |
| RA | 983,147 | C→G | P25A (CCG→GCG) | mepK → | peptidoglycan L,D‑endopeptidase |
| RA | 985,614 | C→G | G32G (GGG→GGC) | aspC ← | aspartate aminotransferase |
| RA | 1,005,691 | T→A | I308I (ATT→ATA) | pyrD → | dihydroorotate dehydrogenase, type 2 |
| RA | 1,005,703 | C→T | A312A (GCC→GCT) | pyrD → | dihydroorotate dehydrogenase, type 2 |
| RA | 1,043,607 | G→A | L202L (CTG→TTG) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,050,092 | C→T | S87L (TCA→TTA) L22L (CTC→CTT) |
insA4 → insB4 → |
IS1 family protein InsA IS1 family protein InsB |
| RA | 1,131,522 | G→A | A29T (GCG→ACG) | flgC → | flagellar basal‑body rod protein FlgC |
| RA | 1,146,079 | C→A | V173F (GTT→TTT) | yceF ← | m(7)GTP pyrophosphatase |
| RA | 1,157,902 | G→T | V12F (GTC→TTC) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| JC JC | 1,190,337 | IS2 (+) +5 bp | coding (107‑111/672 nt) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,195,620 | A→G | K166K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| JC JC | 1,212,703 | IS5 (+) +4 bp | coding (402‑405/405 nt) | ycgX ← | DUF1398 domain‑containing protein YcgX |
| RA | 1,220,493 | C→T | intergenic (+1292/+1812) | ymgF → / ← ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| RA | 1,224,899 | G→A | R155C (CGT→TGT) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,233,669 | G→A | S350F (TCT→TTT) | nhaB ← | Na(+):H(+) antiporter NhaB |
| RA | 1,269,591 | G→A | intergenic (+202/+112) | rdlA → / ← ldrB | putative antisense regulatory RNA RdlA/small toxic polypeptide LdrB |
| RA | 1,290,947 | C→T | Q236* (CAA→TAA) | rssB → | regulator of RpoS |
| RA | 1,292,992 | A→C | intergenic (‑70/‑535) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,463 | C→A | R234S (CGT→AGT) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,318,275 | Δ1 bp | coding (141/1194 nt) | trpB ← | tryptophan synthase subunit beta |
| 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 | 1,371,067 | C→A | G284G (GGC→GGA) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,374,498 | G→T | G137C (GGC→TGC) | ycjP → | putative ABC transporter membrane subunit YcjP |
| RA | 1,405,758 | G→A | intergenic (‑7/‑221) | mcaS ← / → smrA | small regulatory RNA McaS/DNA endonuclease SmrA |
| RA | 1,434,642 | G→A | intergenic (‑236/+543) | ynaM ← / ← uspF | protein YnaM/universal stress protein F |
| RA | 1,442,483 | G→A | H121Y (CAC→TAC) | ldhA ← | D‑lactate dehydrogenase |
| RA | 1,531,689 | A→G | intergenic (‑1185/‑127) | yncO ← / → ydcC | protein YncO/H repeat‑associated putative transposase YdcC |
| RA | 1,553,630 | C→A | G70V (GGT→GTT) | adhP ← | ethanol dehydrogenase/alcohol dehydrogenase |
| RA | 1,555,731 | Δ1 bp | intergenic (‑62/+95) | maeA ← / ← sra | malate dehydrogenase (oxaloacetate‑decarboxylating)/ribosome‑associated protein Sra |
| RA | 1,600,234 | C→T | intergenic (‑25/+54) | lsrK ← / ← lsrR | autoinducer‑2 kinase/DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,098 | C→A | S48S (TCG→TCT) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,103 | C→T | V47M (GTG→ATG) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,632,712 | A→G | intergenic (‑427/‑178) | ydfJ ← / → ynfT | putative transporter YdfJ/protein YnfT |
| RA | 1,632,735 | G→A | intergenic (‑450/‑155) | ydfJ ← / → ynfT | putative transporter YdfJ/protein YnfT |
| RA | 1,641,002 | T→C | intergenic (+27/+337) | ynfU → / ← cspB | putative zinc‑binding protein YnfU/cold shock‑like protein CspB |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,649,971 | C→T | P60S (CCG→TCG) | ydfD → | lysis protein |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,652,518 | IS2 (+) +5 bp | intergenic (+2533/+206) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,697,182 | C→T | intergenic (‑130/+91) | uidR ← / ← hdhA | DNA‑binding transcriptional repressor UidR/7‑alpha‑hydroxysteroid dehydrogenase |
| RA | 1,702,757 | C→T | F175F (TTC→TTT) | add → | adenosine deaminase |
| MC JC | 1,732,136 | Δ7,278 bp | [lhr]–[punR] | [lhr], grxD, mepH, sodB, ydhP, cydH, purR, [punR] | |
| RA | 1,786,745 | G→A | S123F (TCT→TTT) | ppsA ← | phosphoenolpyruvate synthetase |
| RA | 1,793,377 | Δ1 bp | coding (182/750 nt) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,822,296 | G→A | intergenic (‑40/‑162) | osmE ← / → nadE | osmotically‑inducible lipoprotein OsmE/NH3‑dependent NAD(+) synthetase |
| RA | 1,861,311 | C→T | G8S (GGC→AGC) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,874,202 | G→A | intergenic (‑20/‑150) | yoaI ← / → yeaL | protein YoaI/DUF441 domain‑containing inner membrane protein YeaL |
| RA | 1,882,591 | G→A | C227Y (TGC→TAC) | dmlA → | D‑malate/3‑isopropylmalate dehydrogenase (decarboxylating) |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,911,929 | 2 bp→TT | coding (647‑648/882 nt) | htpX ← | protease HtpX |
| RA | 1,915,132 | G→T | P135T (CCG→ACG) | proQ ← | RNA chaperone ProQ |
| RA | 1,915,945 | C→T | G62S (GGC→AGC) | msrC ← | free methionine‑(R)‑sulfoxide reductase |
| RA | 1,929,595 | C→T | G38E (GGA→GAA) | yebE ← | DUF533 domain‑containing inner membrane protein YebE |
| RA | 1,936,634 | C→T | intergenic (‑320/‑18) | zwf ← / → yebK | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase/DNA‑binding transcriptional repressor YebK |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| JC | 2,092,996 | (TGGC)4→3 | coding (599‑602/1071 nt) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,098,825 | C→A | A263A (GCG→GCT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,099,525 | A→T | I30N (ATT→AAT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,155,880 | C→T | L206L (CTC→CTT) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| 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 | 2,190,956 | G→A | D230D (GAC→GAT) | yehC ← | putative fimbrial chaperone YehC |
| RA | 2,191,755 | G→A | Y156Y (TAC→TAT) | yehD ← | putative fimbrial protein YehD |
| RA | 2,192,782 | C→T | W5* (TGG→TGA) | yehE ← | DUF2574 domain‑containing protein YehE |
| RA | 2,198,007 | C→T | intergenic (+709/‑2272) | yehF → / → yehI | PF05406 family protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,199,054 | G→A | intergenic (+1756/‑1225) | yehF → / → yehI | PF05406 family protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,200,887 | G→T | L203L (CTG→CTT) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,202,112 | C→T | L612F (CTC→TTC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,204,047 | C→T | L26F (CTT→TTT) | yehK → | uncharacterized protein YehK |
| RA | 2,205,207 | C→T | T204T (ACC→ACT) | yehL → | putative AAA(+) MoxR family ATPase YehL |
| RA | 2,207,159 | G→A | A489T (GCG→ACG) | yehM → | uncharacterized protein YehM |
| RA | 2,207,546 | G→A | G618S (GGC→AGC) | yehM → | uncharacterized protein YehM |
| RA | 2,224,144 | C→T | V243M (GTG→ATG) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,224,169 | A→G | F234F (TTT→TTC) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,227,313 | G→A | intergenic (‑43/‑1669) | yohF ← / → yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| RA | 2,228,439 | G→A | intergenic (‑1169/‑543) | yohF ← / → yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| RA | 2,230,026 | G→A | Y120Y (TAC→TAT) | dusC ← | tRNA‑dihydrouridine(16) synthase |
| RA | 2,231,616 | G→A | E200K (GAA→AAA) | yohK → | putative 3‑hydroxypropanoate export protein YohK |
| RA | 2,237,105 | G→T | P217T (CCG→ACG) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| JC JC | 2,237,684 | IS5 (+) +4 bp | coding (67‑70/1011 nt) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| RA | 2,264,460 | 2 bp→AT | coding (598‑599/1182 nt) | setB → | sugar exporter SetB |
| RA | 2,272,997 | C→T | P212S (CCG→TCG) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein YejA |
| RA | 2,287,896 | C→T | pseudogene (1019/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,296,636 | G→A | A130V (GCG→GTG) | ccmB ← | cytochrome c maturation protein B |
| RA | 2,319,078 | C→A | D267Y (GAT→TAT) | rcsC ← | histidine kinase RcsC |
| RA | 2,360,550 | Δ1 bp | coding (865/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,392,233 | C→G | G270A (GGT→GCT) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,406,455 | G→A | R63C (CGC→TGC) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,408,858 | C→A | intergenic (+80/‑4) | alaA → / → yfbR | glutamate‑‑pyruvate aminotransferase AlaA/dCMP phosphohydrolase |
| RA | 2,423,891 | C→T | V207I (GTA→ATA) | hisP ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit |
| RA | 2,433,644 | G→A | L95L (CTG→TTG) | accD ← | acetyl‑CoA carboxyltransferase subunit beta |
| RA | 2,443,447 | G→A | A562T (GCG→ACG) | mnmC → | fused tRNA 5‑aminomethyl‑2‑thiouridylate methyltransferase and tRNA 5‑aminomethyl‑2‑thiouridylate synthase |
| RA | 2,473,392 | G→A | intergenic (‑146/‑212) | yfdO ← / → yfdP | protein YdfO/uncharacterized protein YfdP |
| RA | 2,473,397 | +T | intergenic (‑151/‑207) | yfdO ← / → yfdP | protein YdfO/uncharacterized protein YfdP |
| RA | 2,510,609 | C→T | P327L (CCG→CTG) | yfeO → | putative transport protein YfeO |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,630,852 | G→A | S176N (AGC→AAC) | yfgI → | nalidixic acid resistance protein YfgI |
| RA | 2,632,824 | C→T | G416D (GGT→GAT) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,680,713 | C→T | G678E (GGA→GAA) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,684,253 | C→T | intergenic (+197/+1) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator, NAGC‑like/serine hydroxymethyltransferase |
| RA | 2,695,324 | G→C | L74V (CTC→GTC) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,697,981 | C→T | P190P (CCG→CCA) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,698,371 | G→A | R60R (CGC→CGT) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,732,992 | G→A | I394I (ATC→ATT) I394I (ATC→ATT) |
clpB ← clpB ← |
chaperone protein ClpB chaperone protein ClpB |
| RA | 2,739,269 | Δ1 bp | coding (801/1122 nt) | tyrA ← | fused chorismate mutase/prephenate dehydrogenase |
| RA | 2,804,133 | C→T | S211F (TCT→TTT) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,814,459 | Δ1 bp | coding (275/516 nt) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,814,461 | C→T | L91L (CTG→CTA) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,822,099 | G→A | intergenic (‑88/+40) | alaS ← / ← recX | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor/RecA inhibitor RecX |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,871,153 | T→G | N51T (AAC→ACC) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,926,543 | 2 bp→TT | coding (236‑237/1365 nt) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,981,924 | C→T | G87R (GGG→AGG) | araE ← | arabinose:H(+) symporter |
| RA | 2,982,000 | C→T | Q61Q (CAG→CAA) | araE ← | arabinose:H(+) symporter |
| RA | 3,040,842 | 2 bp→AA | coding (228‑229/267 nt) | sdhE ← | FAD assembly factor |
| RA | 3,043,360 | G→A | I88I (ATC→ATT) | yqfB ← | N(4)‑acetylcytidine amidohydrolase |
| RA | 3,071,412 | C→T | intergenic (‑168/+47) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase class II/phosphoglycerate kinase |
| RA | 3,089,109 | A→T | K276* (AAA→TAA) | galP → | galactose:H(+) symporter |
| MC JC | 3,131,341 | Δ8,368 bp | IS5‑mediated | [yghQ]–yghU | [yghQ], yghR, yghS, yghT, pitB, gss, yghU |
| RA | 3,161,616 | G→A | R352C (CGC→TGC) | ftsP ← | cell division protein FtsP |
| RA | 3,167,566 | C→T | V51V (GTG→GTA) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,242,343 | C→T | M324I (ATG→ATA) | uxaA ← | D‑altronate dehydratase |
| RA | 3,270,880 | G→A | S297S (AGC→AGT) | garK ← | glycerate 2‑kinase 1 |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| MC JC | 3,349,206 | Δ16,350 bp | IS5‑mediated | [mtgA]–[yhcE] | [mtgA], elbB, arcZ, arcB, yhcC, gltB, gltD, gltF, yhcA, yhcD, [yhcE] |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,432,105 | C→T | L120L (CTG→CTA) | smg ← | DUF494 domain‑containing protein Smg |
| RA | 3,443,961 | G→A | A46V (GCC→GTC) | secY ← | Sec translocon subunit SecY |
| RA | 3,443,980 | G→A | P40S (CCG→TCG) | secY ← | Sec translocon subunit SecY |
| RA | 3,452,022 | G→A | P89S (CCG→TCG) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,452,218 | G→A | F23F (TTC→TTT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,457,378 | C→T | L334L (CTC→CTT) | gspD → | Type II secretion system protein GspD |
| RA | 3,458,245 | A→C | S623S (TCA→TCC) | gspD → | Type II secretion system protein GspD |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,494,679 | C→T | T223T (ACC→ACT) | nirB → | nitrite reductase (NADH) large subunit |
| 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 | 3,555,047 | G→T | V655F (GTC→TTC) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,555,241 | G→A | R719R (CGG→CGA) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,606,891 | C→T | F147F (TTC→TTT) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,617,379 | T→A | I122K (ATA→AAA) | nikD → | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| RA | 3,624,545 | T→A | D56E (GAT→GAA) | yhhI → | putative transposase |
| RA | 3,647,428 | C→T | A377V (GCG→GTG) | gor → | glutathione reductase (NADPH) |
| 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 | 3,712,407 | G→A | G176G (GGC→GGT) | yhjY ← | putative outer membrane protein YhjY |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,729,955 | 2 bp→AA | coding (810‑811/1323 nt) | xylA ← | xylose isomerase |
| JC JC | 3,731,420 | IS1 (–) +9 bp | coding (290‑298/993 nt) | xylF → | xylose ABC transporter periplasmic binding protein |
| RA | 3,769,447 | G→A | E35K (GAA→AAA) | yibV → | PF15596 family protein YibV |
| RA | 3,773,040 | (G)6→4 | coding (760‑761/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,783,983 | G→A | S49F (TCC→TTC) | secB ← | protein export chaperone SecB |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,833,622 | C→A | D306Y (GAC→TAC) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,865,885 | A→G | V130A (GTT→GCT) | yidE ← | putative transport protein YidE |
| RA | 3,899,195 | C→T | E67K (GAA→AAA) | yieK ← | putative glucosamine‑6‑phosphate deaminase YieK |
| RA | 3,903,234 | G→A | V156V (GTC→GTT) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| 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 | 3,999,664 | C→T | S561L (TCG→TTG) | uvrD → | DNA helicase II |
| RA | 4,009,698 | G→A | A177T (GCA→ACA) | pldB → | lysophospholipase L2 |
| RA | 4,017,197 | C→T | intergenic (+5/‑136) | udp → / → rmuC | uridine phosphorylase/putative recombination limiting protein RmuC |
| RA | 4,084,903 | T→G | N307T (AAC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,092,703 | A→G | F41L (TTC→CTC) | frvA ← | putative PTS enzyme IIA component FrvA |
| MC JC | 4,094,351 | Δ368 bp | intergenic (‑79/+5) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) 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 | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,315,259 | C→T | G94S (GGC→AGC) | phnO ← | aminoalkylphosphonate N‑acetyltransferase |
| RA | 4,315,309 | C→T | G77D (GGC→GAC) | phnO ← | aminoalkylphosphonate N‑acetyltransferase |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,380,105 | G→T | A138E (GCG→GAG) | frdB ← | fumarate reductase iron‑sulfur protein |
| RA | 4,400,254 | C→T | intergenic (+52/‑34) | miaA → / → hfq | tRNA dimethylallyltransferase/RNA‑binding protein Hfq |
| 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 | 4,475,845 | G→A | A137T (GCC→ACC) | yjgL → | protein YjgL |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,516,350 | G→A | P110S (CCA→TCA) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,518,142 | G→A | L32F (CTC→TTC) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,518,221 | G→A | A5A (GCC→GCT) | fecI ← | RNA polymerase sigma factor FecI |
| JC JC | 4,542,042 | IS1 (+) +8 bp | coding (6‑13/597 nt) | fimE → | regulator for fimA |
| RA | 4,545,746 | T→C | I217I (ATT→ATC) | fimD → | type I fimbriae usher protein |
| 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 | 1196302 | 1211447 | 15146 | 30 [29] | [29] 30 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1411925 | 1433822–1433669 | 21745–21898 | 90 [0] | [26] 30 | [ttcA]–pinR | [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 |
| * | * | ÷ | NC_000913 | 1434698 | 1434984 | 287 | 30 [29] | [7] 97 | ynaM/uspF | protein YnaM/universal stress protein F |
| * | * | ÷ | NC_000913 | 1632742 | 1633400–1633224 | 483–659 | 30 [29] | [29] 30 | ynfT–ydfK | ynfT,ydfK |
| * | * | ÷ | NC_000913 | 2947468 | 2947684 | 217 | 68 [0] | [29] 30 | metW–metV | metW,metV |
| * | * | ÷ | NC_000913 | 3423824–3424233 | 3424476–3424239 | 7–653 | 30 [29] | [29] 30 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3762389–3764074 | 3765153–3764083 | 10–2765 | 30 [29] | [29] 30 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 4038053–4038686 | 4039164–4038691 | 6–1112 | 31 [29] | [29] 30 | rrlA | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 133 (1.440) | 86/590 | 0.0 | 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 | = 1411924 | 0 (0.000) | 90 (1.050) | 61/546 | 0.2 | 100% | coding (25/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | 1434985 = | 0 (0.000) | intergenic (‑579/+200) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 2947467 | 0 (0.000) | 68 (1.000) | 43/432 | 0.3 | 100% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 0 (0.000) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | 4542682 = | 29 (0.310) | 126 (1.380) | 72/580 | 0.1 | 85.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 14 (0.150) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 42 (0.450) | 128 (1.410) | 72/580 | 0.1 | 82.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 14 (0.150) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||