mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 36,231 | T→C | intergenic (‑69/+40) | caiD ← / ← caiC | carnitinyl‑CoA dehydratase/putative crotonobetaine/carnitine‑CoA ligase |
| RA | 53,012 | A→G | G135G (GGT→GGC) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 88,208 | A→T | T61S (ACA→TCA) | cra → | transcriptional repressor‑activator for carbon metabolism |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 129,360 | G→T | intergenic (+24/+47) | lpd → / ← yacH | dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase/DUF3300 family protein |
| RA | 160,736 | A→T | intergenic (‑132/+46) | dksA ← / ← sfsA | transcriptional regulator of rRNA transcription; DnaK suppressor protein/sugar fermentation stimulation protein A |
| RA | 162,973 | G→A | C290Y (TGT→TAT) | hrpB → | putative ATP‑dependent helicase |
| RA | 178,902 | C→T | L84L (TTG→TTA) | mtn ← | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase |
| RA | 179,327 | A→T | I31F (ATC→TTC) | dgt → | deoxyguanosine triphosphate triphosphohydrolase |
| RA | 179,442 | A→T | H69L (CAC→CTC) | dgt → | deoxyguanosine triphosphate triphosphohydrolase |
| JC | 190,553 | Δ14 bp | coding (680‑693/726 nt) | rpsB → | 30S ribosomal subunit protein S2 |
| RA | 194,128 | C→T | P203L (CCG→CTG) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| RA | 216,568 | C→T | A146T (GCC→ACC) | yaeF ← | putative lipoprotein |
| RA | 232,196 | G→T | G91C (GGC→TGC) | yafE → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 236,541 | C→T | R159* (CGA→TGA) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 265,418 | A→G | R42R (CGT→CGC) | ykfF ← | CP4‑6 prophage; uncharacterized protein |
| RA | 281,581 | G→A | R135W (CGG→TGG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 362,884 | A→G | L99S (TTA→TCA) | lacY ← | lactose permease |
| RA | 364,024 | C→T | R761H (CGC→CAC) | lacZ ← | beta‑D‑galactosidase |
| RA | 367,830 | G→A | Y197Y (TAC→TAT) | mhpR ← | mhp operon transcriptional activator |
| RA | 383,477 | G→A | G153G (GGC→GGT) | yaiP ← | putative family 2 glycosyltransferase |
| RA | 400,214 | T→C | D237G (GAC→GGC) | ddlA ← | D‑alanine‑D‑alanine ligase A |
| RA | 416,389 | (C)5→4 | coding (564/1203 nt) | sbcD ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 428,188 | G→T | R181L (CGC→CTC) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 459,256 | T→C | D123D (GAT→GAC) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 459,642 | A→G | E252G (GAA→GGA) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 497,139 | (T)5→6 | intergenic (+145/‑36) | htpG → / → adk | protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase/adenylate kinase |
| RA | 520,993 | T→G | V193G (GTC→GGC) | ybbP → | putative ABC transporter permease |
| RA | 532,380 | A→G | intergenic (‑159/‑71) | allS ← / → allA | allD operon transcriptional activator/ureidoglycolate lyase, releasing urea |
| RA | 584,262 | (A)7→8 | coding (582/750 nt) | appY → | global transcriptional activator; DLP12 prophage |
| RA | 627,309 | G→A | G414S (GGC→AGC) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase component of enterobactin synthase multienzyme complex |
| RA | 649,964 | +G | coding (527/909 nt) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 661,369 | T→C | N4D (AAT→GAT) | ybeF ← | LysR family putative transcriptional regulator |
| RA | 662,636 | T→G | T3P (ACC→CCC) | ybeD ← | UPF0250 family protein |
| RA | 700,805 | A→T | C264S (TGC→AGC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 712,150 | A→T | L218Q (CTG→CAG) | ybfF ← | acyl‑CoA esterase |
| RA | 720,946 | C→T | intergenic (+106/+110) | ybfK → / ← kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| RA | 750,896 | Δ1 bp | coding (1274/2448 nt) | ybgQ ← | putative outer membrane protein |
| RA | 772,209 | C→A | T251N (ACC→AAC) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 834,352 | A→T | Q428L (CAG→CTG) | dinG → | ATP‑dependent DNA helicase |
| RA | 851,094 | G→A | P502S (CCG→TCG) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 882,722 | G→A | R5C (CGC→TGC) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
| RA | 894,155 | T→G | D124E (GAT→GAG) | potF → | putrescine ABC transporter periplasmic binding protein |
| RA | 905,720 | C→A | L270M (CTG→ATG) | amiD → | 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent; OM lipoprotein |
| RA | 931,952 | C→T | V33V (GTG→GTA) | trxB ← | thioredoxin reductase, FAD/NAD(P)‑binding |
| RA | 933,387 | C→T | A55V (GCC→GTC) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 966,368 | A→G | A683A (GCA→GCG) | ycaI → | ComEC family inner membrane protein |
| RA | 975,083 | T→A | D255E (GAT→GAA) | mukF → | chromosome condensin MukBEF, kleisin‑like subunit, binds calcium |
| RA | 1,017,296 | A→C | I335S (ATC→AGC) | ycbZ ← | putative peptidase |
| RA | 1,065,426 | A→T | intergenic (+134/‑159) | yccE → / → agp | uncharacterized protein/glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,068,621 | T→A | T407S (ACG→TCG) | rutG ← | pyrimidine permease |
| RA | 1,073,307 | Δ1 bp | coding (705/1149 nt) | rutA ← | pyrimidine oxygenase, FMN‑dependent |
| RA | 1,097,209 | T→G | intergenic (+380/+356) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,100,233 | G→A | intergenic (+39/‑63) | ycdY → / → ycdZ | redox enzyme maturation protein (REMP) chaperone for YcdX/DUF1097 family inner membrane protein |
| RA | 1,111,377 | A→G | D172G (GAT→GGT) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,143,125 | C→T | D415N (GAC→AAC) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,170,338 | (A)6→5 | coding (37/963 nt) | ldtC ← | L,D‑transpeptidase linking Lpp to murein |
| RA | 1,197,340 | T→C | T65A (ACT→GCT) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,197,739 | A→G | S167P (TCC→CCC) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,207,981 | G→A | A161T (GCC→ACC) | stfP → | e14 prophage; uncharacterized protein |
| RA | 1,292,944 | T→C | intergenic (‑22/‑583) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,196 | IS5 (+) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,307,634 | T→A | I338F (ATC→TTC) | clsA ← | cardiolipin synthase 1 |
| RA | 1,369,793 | G→A | E35E (GAG→GAA) | pspE → | thiosulfate:cyanide sulfurtransferase (rhodanese) |
| RA | 1,382,820 | T→C | Y292H (TAT→CAT) | ompG → | outer membrane porin G |
| RA | 1,399,677 | C→T | intergenic (‑151/+44) | fnr ← / ← ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,401,844 | A→G | I471T (ATC→ACC) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,407,859 | A→G | intergenic (‑64/‑191) | ydaM ← / → ydaN | diguanylate cyclase, csgD regulator/putative Zn(II) transporter |
| RA | 1,433,718 | T→C | intergenic (‑44/+273) | pinR ← / ← ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| RA | 1,434,459 | C→T | intergenic (‑235/+499) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| RA | 1,435,737 | G→A | intergenic (‑118/+23) | uspF ← / ← ompN | stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific |
| RA | 1,448,947 | A→C | T477P (ACG→CCG) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,470,558 | G→A | pseudogene (42/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,493,774 | A→G | L435L (TTA→TTG) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,501,912 | T→A | I117I (ATT→ATA) | tehB → | tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein |
| RA | 1,530,076 | (A)7→8 | coding (155/483 nt) | ydcD → | putative immunity protein for RhsE |
| RA | 1,547,395 | A→G | intergenic (‑226/‑6) | yddG ← / → fdnG | aromatic amino acid exporter/formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,555,324 | A→G | S116P (TCT→CCT) | maeA ← | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| RA | 1,580,094 | C→T | D233N (GAT→AAT) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,650,904 | T→C | pseudogene (60/693 nt) | insD1 → | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,658,592 | C→T | A175V (GCC→GTC) | ynfE → | putative selenate reductase, periplasmic |
| RA | 1,665,195 | (T)7→8 | intergenic (+75/‑120) | dmsD → / → clcB | twin‑argninine leader‑binding protein for DmsA and TorA/H(+)/Cl(‑) exchange transporter |
| RA | 1,681,932 | T→C | P33P (CCA→CCG) | ydgC ← | GlpM family inner membrane protein |
| RA | 1,707,029 | A→G | V37V (GTA→GTG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,712,306 | (T)7→8 | intergenic (+148/‑463) | nth → / → dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| RA | 1,712,518 | (C)6→5 | intergenic (+360/‑251) | nth → / → dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| RA | 1,728,444 | C→A | T33N (ACC→AAC) | rnt → | RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair |
| RA | 1,827,031 | T→A | D410V (GAT→GTT) | astB ← | succinylarginine dihydrolase |
| RA | 1,880,549 | T→C | T71A (ACC→GCC) | leuE ← | leucine efflux protein |
| RA | 1,881,128 | C→A | E228* (GAA→TAA) | dmlR ← | transcriptional activator of dmlA |
| RA | 1,946,790 | T→G | G180G (GGT→GGG) | yebB → | DUF830 family protein |
| RA | 1,971,761 | T→C | T311A (ACC→GCC) | tar ← | methyl‑accepting chemotaxis protein II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,983,761 | C→T | E437K (GAA→AAA) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 2,071,321 | A→G | intergenic (+110/‑218) | yeeP → / → flu | pseudogene, CP4‑44 prophage; 50S ribosome‑binding GTPase family;Phage or Prophage Related; putative histone/CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,159,354 | C→T | R323R (CGC→CGT) | mdtC → | multidrug efflux system, subunit C |
| RA | 2,161,946 | A→G | A161A (GCA→GCG) | iceT → | putative citrate/iron‑citrate/zinc‑citrate efflux transporter |
| RA | 2,173,076 | C→A | pseudogene (287/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,191,432 | C→T | G72S (GGC→AGC) | yehC ← | putative periplasmic pilin chaperone |
| RA | 2,197,365 | G→A | pseudogene (892/2847 nt) | yehH → | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| RA | 2,210,811 | C→T | pseudogene (1712/2001 nt) | yehQ → | pseudogene |
| RA | 2,235,656 | T→C | I131T (ATC→ACC) | preA → | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C |
| RA | 2,246,800 | A→G | intergenic (‑31/+263) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,250,210 | T→A | V165E (GTG→GAG) | yeiH → | UPF0324 family inner membrane protein |
| RA | 2,278,298 | C→T | intergenic (‑61/+272) | yejG ← / ← bcr | uncharacterized protein/bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,279,021 | G→A | A247V (GCG→GTG) | bcr ← | bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,307,386 | A→T | D410E (GAT→GAA) | yojI ← | microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,361,323 | T→A | Q31L (CAG→CTG) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,386,365 | T→A | F169Y (TTC→TAC) | yfbL → | putative M28A family peptidase |
| RA | 2,411,637 | Δ1 bp | coding (453/651 nt) | yfbT ← | sugar phosphatas |
| RA | 2,420,727 | G→A | G36D (GGC→GAC) | yfcG → | GSH‑dependent disulfide bond oxidoreductase |
| RA | 2,436,937 | A→T | D305E (GAT→GAA) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,469,656 | (T)7→8 | coding (526/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,493,645 | G→A | intergenic (‑391/+122) | frc ← / ← yfdX | formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein |
| RA | 2,495,173 | T→A | A40A (GCA→GCT) | yfdY ← | DUF2545 family putative inner membrane protein |
| RA | 2,521,967 | C→A | A171S (GCG→TCG) | xapR ← | transcriptional activator of xapAB |
| RA | 2,525,135 | (A)6→5 | coding (9/765 nt) | yfeN → | putative outer membrane protein |
| RA | 2,530,925 | T→C | Q103Q (CAA→CAG) | zipA ← | FtsZ stabilizer |
| RA | 2,534,206 | T→G | R47R (CGT→CGG) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,541,456 | A→G | I75T (ATT→ACT) | cysW ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,563,518 | (A)5→6 | intergenic (+401/‑74) | yffP → / → yffQ | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,564,525 | G→A | M1M (ATG→ATA) † | yffS → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,593,917 | G→A | A648V (GCG→GTG) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
| RA | 2,600,288 | C→T | S128L (TCG→TTG) | gcvR → | transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,638,037 | C→A | A206S (GCG→TCG) | bamB ← | BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,644,169 | G→T | P39T (CCC→ACC) | rlmN ← | dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent |
| RA | 2,758,577 | G→T | N8K (AAC→AAA) | yfjH ← | CP4‑57 prophage; uncharacterized protein |
| RA | 2,777,363 | T→C | F83F (TTT→TTC) | yfjZ → | CP4‑57 prophage; antitoxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,810,756 | G→A | intergenic (+77/‑14) | ygaH → / → mprA | putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,852,356 | T→A | L74Q (CTG→CAG) | hypD → | hydrogenase maturation protein |
| RA | 2,867,164 | C→T | A130T (GCG→ACG) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,887,352 | T→A | intergenic (‑133/+226) | ygcB ← / ← cysH | Cascade complex anti‑viral R‑loop helicase‑annealase Cas3/phosphoadenosine phosphosulfate reductase; PAPS reductase, thioredoxin dependent |
| RA | 2,900,481 | G→T | intergenic (‑208/‑111) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,966,414 | T→G | D674A (GAT→GCT) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,041,028 | G→A | R15C (CGT→TGT) | sdhE ← | flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair |
| RA | 3,150,120 | T→C | F153F (TTT→TTC) | yghA → | putative oxidoreductase |
| RA | 3,165,015 | T→A | D320V (GAT→GTT) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,350,648 | T→A | intergenic (‑189/+41) | elbB ← / ← arcB | isoprenoid biosynthesis protein with amidotransferase‑like domain/aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,443,086 | T→A | N338Y (AAC→TAC) | secY ← | preprotein translocase membrane subunit |
| RA | 3,452,057 | A→T | I77N (ATC→AAC) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,477,434 | T→C | intergenic (‑15/‑206) | fkpA ← / → slyX | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)/phi X174 lysis protein |
| RA | 3,524,413 | A→G | I515V (ATT→GTT) | mrcA → | penicillin‑binding protein 1a, murein transglycosylase and transpeptidase |
| RA | 3,541,962 | T→G | I519S (ATC→AGC) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,597,846 | (T)5→4 | intergenic (‑286/‑138) | livK ← / → panM | leucine transporter subunit/PanD autocleavage accelerator, panothenate synthesis |
| RA | 3,622,796 | T→G | L1202R (CTG→CGG) | rhsB → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 3,648,042 | T→C | intergenic (‑254/‑486) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| RA | 3,669,340 | A→G | intergenic (‑152/‑252) | yhjA ← / → treF | putative cytochrome C peroxidase/cytoplasmic trehalase |
| RA | 3,669,920 | A→G | E110G (GAA→GGA) | treF → | cytoplasmic trehalase |
| RA | 3,708,410 | T→A | intergenic (‑705/+206) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,746,162 | G→T | L23L (CTG→CTT) | yiaO → | 2,3‑diketo‑L‑gulonate‑binding periplasmic protein |
| RA | 3,770,087 | C→A | pseudogene (55/114 nt) | yibU → | pseudogene, H repeat‑associated protein |
| RA | 3,805,475 | T→C | N159S (AAT→AGT) | waaP ← | kinase that phosphorylates core heptose of lipopolysaccharide |
| RA | 3,822,694 | G→T | G99W (GGG→TGG) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,840,547 | T→C | intergenic (+39/+2) | yicS → / ← nepI | putative periplasmic protein/putative transporter |
| RA | 3,853,909 | A→G | intergenic (+267/‑13) | tisB → / → emrD | toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein |
| RA | 3,906,597 | C→A | intergenic (‑30/+256) | bglG ← / ← phoU | transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator |
| RA | 3,910,662 | A→T | D288E (GAT→GAA) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,927,735 | Δ1 bp | coding (581/993 nt) | asnA → | asparagine synthetase A |
| RA | 3,950,468 | G→T | intergenic (+48/‑39) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 3,971,690 | A→C | Q144P (CAG→CCG) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 4,017,924 | G→A | D198N (GAC→AAC) | rmuC → | DNA recombination protein |
| RA | 4,098,512 | C→A | R259R (CGC→CGA) | rhaS → | transcriptional activator of rhaBAD and rhaT |
| RA | 4,152,760 | G→T | N113K (AAC→AAA) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,168,540 | T→A | intergenic (+93/‑101) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,178,296 | A→T | intergenic (+8/‑151) | nusG → / → rplK | transcription termination factor/50S ribosomal subunit protein L11 |
| RA | 4,235,689 | +A | intergenic (+282/‑217) | pgi → / → yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,238,726 | A→G | I365V (ATT→GTT) | yjbH → | DUF940 family extracellular polysaccharide protein |
| MC JC | 4,242,942 | Δ66 bp | coding (510‑575/891 nt) | malG ← | maltose transporter subunit |
| RA | 4,279,370 | G→T | A298S (GCA→TCA) | ghxP → | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| RA | 4,289,526 | A→G | K94K (AAA→AAG) | nrfB → | nitrite reductase, formate‑dependent, penta‑heme cytochrome c |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,340,287 | G→A | L79F (CTT→TTT) | adiA ← | arginine decarboxylase |
| RA | 4,352,460 | T→G | intergenic (+103/‑124) | yjdJ → / → ghoS | GNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA |
| RA | 4,358,482 | T→A | I46F (ATC→TTC) | cadA ← | lysine decarboxylase, acid‑inducible |
| RA | 4,360,814 | T→G | Y374S (TAC→TCC) | cadC ← | cadBA operon transcriptional activator |
| JC | 4,370,611 | Δ5 bp | intergenic (‑199/‑73) | yjeH ← / → groS | putative transporter/Cpn10 chaperonin GroES, small subunit of GroESL |
| RA | 4,478,879 | T→C | V136A (GTT→GCT) | rraB → | protein inhibitor of RNase E |
| RA | 4,490,055 | T→G | E3D (GAA→GAC) | yjgR ← | DUF853 family protein with NTPase fold |
| RA | 4,500,814 | Δ1 bp | intergenic (‑23/‑446) | yjgX ← / → yjgZ | pseudogene fragment/uncharacterized protein |
| RA | 4,547,319 | C→A | R742S (CGT→AGT) | fimD → | fimbrial usher outer membrane porin protein; FimCD chaperone‑usher |
| RA | 4,615,859 | T→G | T403P (ACC→CCC) | yjjI ← | DUF3029 family protein, putative glycine radical enzyme |
| RA | 4,627,837 | A→T | I175F (ATC→TTC) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,631,700 | T→C | L323P (CTT→CCT) | slt → | lytic murein transglycosylase, soluble |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423705–3424234 | 3424607–3424238 | 5–903 | 81 [79] | [79] 80 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 183 (1.400) | 107/190 | 0.0 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||