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 | freq | annotation | gene | description |
| RA | 44,352 | Δ1 bp | 5.3% | coding (173/1287 nt) | fixC → | putative oxidoreductase |
| RA | 139,753 | C→T | 5.2% | P163L (CCG→CTG) | yadG → | putative ABC superfamily transporter ATP‑binding subunit |
| RA | 183,224 | C→G | 5.3% | R638R (CGG→CGC) ‡ | glnD ← | uridylyltransferase |
| RA | 183,225 | C→G | 5.1% | R638P (CGG→CCG) ‡ | glnD ← | uridylyltransferase |
| RA | 243,106 | A→T | 5.2% | intergenic (‑117/‑93) | dinJ ← / → yafL | antitoxin of YafQ‑DinJ toxin‑antitoxin system/putative lipoprotein and C40 family peptidase |
| RA | 243,108 | A→C | 5.2% | intergenic (‑119/‑91) | dinJ ← / → yafL | antitoxin of YafQ‑DinJ toxin‑antitoxin system/putative lipoprotein and C40 family peptidase |
| RA | 243,109 | T→A | 7.7% | intergenic (‑120/‑90) | dinJ ← / → yafL | antitoxin of YafQ‑DinJ toxin‑antitoxin system/putative lipoprotein and C40 family peptidase |
| RA | 327,648 | C→A | 5.7% | intergenic (+441/‑434) | betT → / → yahA | choline transporter of high affinity/c‑di‑GMP‑specific phosphodiesterase |
| RA | 445,212 | C→T | 100% | G296S (GGT→AGT) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 448,074 | A→T | 5.1% | S310T (TCG→ACG) | ampG ← | muropeptide transporter |
| RA | 576,057 | T→A | 6.7% | intergenic (‑156/‑233) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein |
| RA | 637,949 | G→A | 5.1% | V136I (GTT→ATT) | ybdR → | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 679,476 | G→T | 5.7% | A131A (GCC→GCA) | rihA ← | ribonucleoside hydrolase 1 |
| RA | 844,523 | G→A | 5.2% | intergenic (‑156/+143) | dps ← / ← rhtA | Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system |
| RA | 844,531 | C→T | 5.8% | intergenic (‑164/+135) | dps ← / ← rhtA | Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system |
| RA | 844,532 | A→T | 5.9% | intergenic (‑165/+134) | dps ← / ← rhtA | Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system |
| RA | 844,533 | A→G | 5.9% | intergenic (‑166/+133) | dps ← / ← rhtA | Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system |
| RA | 871,320 | T→G | 5.0% | M177R (ATG→AGG) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 871,327 | T→G | 5.0% | S179S (TCT→TCG) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 982,874 | A→T | 8.0% | intergenic (‑436/+167) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 982,876 | A→C | 8.4% | intergenic (‑438/+165) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 982,877 | A→T | 8.4% | intergenic (‑439/+164) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 982,878 | G→T | 9.1% | intergenic (‑440/+163) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 982,880 | A→T | 11.2% | intergenic (‑442/+161) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,006,105 | G→T | 5.4% | G229V (GGC→GTC) | uup → | putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 1,034,936 | T→A | 5.5% | V62D (GTC→GAC) | cbdB → | cytochrome bd‑II oxidase, subunit II |
| RA | 1,071,903 | C→T | 5.6% | A812A (GCG→GCA) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,209,579 | A→T | 6.7% | intergenic (‑64/+141) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,209,581 | A→T | 6.7% | intergenic (‑66/+139) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,209,582 | C→A | 6.9% | intergenic (‑67/+138) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,209,585 | T→G | 6.8% | intergenic (‑70/+135) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,209,586 | A→T | 6.8% | intergenic (‑71/+134) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,209,588 | A→T | 6.7% | intergenic (‑73/+132) | bluR ← / ← bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| RA | 1,268,685 | A→T | 7.4% | intergenic (+27/+17) | chaC → / ← ychN | cation transport regulator/putative sulfur relay protein |
| RA | 1,288,276 | C→A | 100% | V35F (GTT→TTT) | hns ← | global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,294,723:1 | +A | 5.1% | intergenic (+22/‑716) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| RA | 1,294,726 | C→G | 5.1% | intergenic (+25/‑713) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| RA | 1,294,729 | Δ1 bp | 5.2% | intergenic (+28/‑710) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| RA | 1,294,756 | A→T | 5.3% | intergenic (+55/‑683) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| RA | 1,301,044 | G→A | 5.1% | intergenic (+19/+34) | oppF → / ← yciU | oligopeptide transporter subunit/UPF0263 family protein |
| RA | 1,301,045 | T→C | 5.1% | intergenic (+20/+33) | oppF → / ← yciU | oligopeptide transporter subunit/UPF0263 family protein |
| RA | 1,340,781 | G→T | 5.7% | S73R (AGC→AGA) | gmr ← | cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability |
| RA | 1,401,304 | T→C | 5.3% | E250G (GAA→GGA) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,458,118 | G→T | 5.6% | G108V (GGT→GTT) | paaX → | transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,461,884 | G→A | 7.0% | pseudogene (2236/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,887 | A→C | 7.5% | pseudogene (2239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,892 | G→T | 7.4% | pseudogene (2244/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,465,206 | G→T | 5.3% | pseudogene (433/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,465,209 | A→C | 5.4% | pseudogene (436/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,465,214 | G→T | 5.3% | pseudogene (441/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,465,217 | A→C | 5.3% | pseudogene (444/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,475,343 | C→T | 5.6% | L60L (CTG→TTG) | ynbD → | putative phosphatase inner membrane protein |
| RA | 1,532,531 | T→C | 5.6% | T194A (ACC→GCC) | narY ← | nitrate reductase 2 (NRZ), beta subunit |
| RA | 1,556,606 | G→T | 6.1% | P45T (CCG→ACG) | ddpA ← | D‑ala‑D‑a la transporter subunit |
| RA | 1,635,978 | C→T | 5.2% | intergenic (‑167/‑134) | cspB ← / → cspF | Qin prophage; cold shock protein/Qin prophage; cold shock protein |
| RA | 1,745,915 | G→A | 6.7% | R23W (CGG→TGG) | ydhW ← | FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,765,107 | G→A | 5.3% | R79H (CGT→CAT) | ydiL → | putative HTH domain DNA‑binding protein |
| RA | 1,796,550 | G→A | 5.5% | A93V (GCA→GTA) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,802,643 | C→T | 7.7% | G197G (GGC→GGT) | yniA → | fructosamine kinase family protein |
| RA | 1,837,502 | G→A | 5.1% | R292Q (CGA→CAA) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,844,972 | Δ1 bp | 5.6% | intergenic (+22/‑145) | sppA → / → ansA | protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1 |
| RA | 1,844,976:1 | +T | 5.7% | intergenic (+26/‑141) | sppA → / → ansA | protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1 |
| RA | 1,894,928 | C→G | 5.4% | T305T (ACG→ACC) ‡ | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,894,929 | G→A | 5.4% | T305M (ACG→ATG) ‡ | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,939,821 | T→C | 5.1% | D138G (GAT→GGT) | ruvA ← | component of RuvABC resolvasome, regulatory subunit |
| RA | 2,076,729 | C→G | 6.7% | R165G (CGC→GGC) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,096,552 | C→T | 5.1% | pseudogene (319/446 nt) | wbbL ← | lipopolysaccharide biosynthesis protein, N‑ter fragment (pseudogene) |
| RA | 2,096,560 | T→A | 5.6% | pseudogene (311/446 nt) | wbbL ← | lipopolysaccharide biosynthesis protein, N‑ter fragment (pseudogene) |
| RA | 2,096,562 | A→T | 5.5% | pseudogene (309/446 nt) | wbbL ← | lipopolysaccharide biosynthesis protein, N‑ter fragment (pseudogene) |
| RA | 2,096,564 | T→A | 6.1% | pseudogene (307/446 nt) | wbbL ← | lipopolysaccharide biosynthesis protein, N‑ter fragment (pseudogene) |
| RA | 2,134,465 | G→A | 5.1% | S210F (TCT→TTT) | asmA ← | suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,234,957 | A→T | 5.1% | V64E (GTG→GAG) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,244,650 | G→T | 7.0% | G111V (GGC→GTC) | nfo → | endonuclease IV with intrinsic 3'‑5' exonuclease activity |
| RA | 2,306,688 | C→G | 5.3% | intergenic (+33/‑279) | micF → / → rcsD | sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,421,178 | T→A | 5.2% | G31G (GGA→GGT) | argT ← | lysine/arginine/ornithine transporter subunit |
| RA | 2,600,747 | C→T | 6.7% | Q158* (CAG→TAG) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,641,811 | C→A | 5.6% | G1279V (GGT→GTT) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,693,193 | A→T | 6.3% | N58Y (AAT→TAT) | yfhL → | putative 4Fe‑4S cluster‑containing protein |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,831,581 | A→T | 6.1% | intergenic (‑117/+32) | hydN ← / ← ascG | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,831,590 | A→T | 5.9% | intergenic (‑126/+23) | hydN ← / ← ascG | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,926,412 | T→A | 6.0% | R212R (CGA→CGT) | fucA ← | L‑fuculose‑1‑phosphate aldolase |
| RA | 2,979,854 | G→T | 5.7% | D217Y (GAC→TAC) | yqeG → | putative transporter |
| RA | 3,000,256 | C→T | 5.4% | I212I (ATC→ATT) | ygeW → | putative carbamoyltransferase |
| RA | 3,041,538 | G→A | 7.3% | A288V (GCG→GTG) | gcvP ← | glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,050,504 | G→C | 5.0% | intergenic (+157/+33) | sibC → / ← serA | sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,050,509 | C→T | 5.1% | intergenic (+162/+28) | sibC → / ← serA | sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,072,806 | A→G | 100% | intergenic (‑117/+197) | cmtB ← / ← tktA | putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding |
| RA | 3,129,987 | T→G | 5.3% | intergenic (‑257/+35) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,129,988 | C→A | 5.1% | intergenic (‑258/+34) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,129,989 | T→A | 5.1% | intergenic (‑259/+33) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,129,990 | T→G | 5.1% | intergenic (‑260/+32) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,129,991 | C→A | 5.1% | intergenic (‑261/+31) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,147,337 | T→C | 5.1% | L139P (CTG→CCG) | yghB → | general envelope maintenance protein; DedA family inner membrane protein |
| RA | 3,203,333 | A→G | 5.1% | G190G (GGT→GGC) | tsaD ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein |
| RA | 3,261,813 | G→T | 6.0% | D14Y (GAT→TAT) | yhaC → | pentapetide repeats‑related protein |
| RA | 3,334,569 | G→T | 5.4% | W312C (TGG→TGT) | yrbG → | putative calcium/sodium:proton antiporter |
| RA | 3,343,073 | C→T | 5.3% | A32A (GCG→GCA) | mtgA ← | biosynthetic peptidoglycan transglycosylase |
| RA | 3,391,459 | C→A | 7.3% | L93F (TTG→TTT) | yhdE ← | Maf‑like protein |
| RA | 3,416,588 | T→G | 5.5% | intergenic (+35/+194) | yhdZ → / ← rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| RA | 3,471,372 | T→A | 6.7% | H162L (CAC→CTC) | slyD ← | FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase) |
| RA | 3,485,064 | A→C | 6.1% | intergenic (‑85/+20) | yhfG ← / ← ppiA | putative Fic‑binding protein/peptidyl‑prolyl cis‑trans isomerase A (rotamase A) |
| RA | 3,648,187 | A→T | 6.9% | M49L (ATG→TTG) ‡ | dctR → | LuxR family putative transcriptional regulator |
| RA | 3,648,189 | G→C | 6.8% | M49I (ATG→ATC) ‡ | dctR → | LuxR family putative transcriptional regulator |
| RA | 3,648,191 | A→T | 7.2% | N50I (AAT→ATT) | dctR → | LuxR family putative transcriptional regulator |
| RA | 3,751,350 | T→A | 6.3% | intergenic (‑163/+27) | yiaY ← / ← selB | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family/selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,751,352 | T→G | 6.7% | intergenic (‑165/+25) | yiaY ← / ← selB | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family/selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,751,356 | A→T | 6.0% | intergenic (‑169/+21) | yiaY ← / ← selB | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family/selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,751,360 | C→A | 6.6% | intergenic (‑173/+17) | yiaY ← / ← selB | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family/selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,781,163 | T→A | 5.1% | G322G (GGT→GGA) | envC → | activator of AmiB,C murein hydrolases, septal ring factor |
| RA | 3,804,054 | C→T | 5.1% | A153A (GCG→GCA) | mutM ← | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase |
| RA | 3,908,605 | C→G | 5.8% | intergenic (‑45/+308) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,606 | T→A | 5.5% | intergenic (‑46/+307) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,617 | A→G | 5.1% | intergenic (‑57/+296) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,618 | C→T | 5.1% | intergenic (‑58/+295) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,620 | T→G | 5.2% | intergenic (‑60/+293) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,629 | T→A | 5.1% | intergenic (‑69/+284) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,908,630 | C→G | 5.2% | intergenic (‑70/+283) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,918,162 | G→A | 5.3% | P278S (CCG→TCG) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,970,739 | G→T | 5.1% | V368F (GTC→TTC) | wzxE → | O‑antigen translocase |
| RA | 3,970,742 | A→C | 5.1% | S369R (AGC→CGC) | wzxE → | O‑antigen translocase |
| RA | 3,978,322 | G→T | 6.0% | T349K (ACG→AAG) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 3,978,325 | T→A | 6.1% | N348I (AAC→ATC) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 3,978,328 | T→A | 5.9% | D347V (GAT→GTT) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 3,978,331 | A→C | 6.1% | L346R (CTT→CGT) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 3,978,337 | C→T | 6.0% | G344D (GGT→GAT) | aslA ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 4,012,221 | G→T | 6.0% | D3Y (GAT→TAT) | ubiE → | bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase/ S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,134,564 | G→T | 5.2% | A214A (GCG→GCT) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,199,979 | G→A | 5.6% | noncoding (9/2904 nt) | rrlE → | 23S ribosomal RNA of rrnE operon |
| RA | 4,269,160 | G→A | 5.1% | A252T (GCG→ACG) | yjcD → | inner membrane putative guanine permease |
| RA | 4,356,367 | T→C | 5.4% | Q75R (CAG→CGG) | dcuA ← | C4‑dicarboxylate antiporter |
| RA | 4,509,128 | A→G | 5.1% | intergenic (+87/+27) | insB1 → / ← yjhU | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element |
| RA | 4,561,269 | G→A | 100% | S41S (AGC→AGT) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 4323060 | 4323814 | 755 | 42 [39] | [38] 40 | [basS]–[eptA] | [basS],basR,[eptA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 75231 = | 85 (0.990) | 4 (0.050) | 4/232 | NT | 5.1% | coding (1124/1179 nt) | setA | broad specificity sugar efflux system |
| ? | CP009273 | 75270 = | 70 (0.880) | coding (1163/1179 nt) | setA | broad specificity sugar efflux system | |||||
| * | ? | CP009273 | = 196816 | 59 (0.690) | 4 (0.050) | 4/238 | NT | 6.1% | coding (2402/2433 nt) | bamA | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| ? | CP009273 | = 196848 | 66 (0.810) | intergenic (+1/‑121) | bamA/skp | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor/periplasmic chaperone | |||||
| * | ? | CP009273 | 223191 = | NA (NA) | 5 (0.060) | 5/242 | NT | NA | noncoding (946/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | 223217 = | NA (NA) | noncoding (972/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 223984 = | NA (NA) | 6 (0.070) | 4/240 | NT | NA | noncoding (1739/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | 224011 = | NA (NA) | noncoding (1766/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 224583 = | NA (NA) | 3 (0.040) | 3/246 | NT | NA | noncoding (2338/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | 224629 = | NA (NA) | noncoding (2384/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | = 227466 | 69 (0.800) | 4 (0.050) | 4/246 | NT | 5.6% | intergenic (‑98/‑143) | yafC/yafD | LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein |
| ? | CP009273 | = 227523 | 68 (0.800) | intergenic (‑155/‑86) | yafC/yafD | LysR family putative transcriptional regulator/endo/exonuclease/phosphatase family protein | |||||
| * | ? | CP009273 | = 266798 | NA (NA) | 4 (0.050) | 4/244 | NT | NA | coding (485/1152 nt) | insI1 | IS30 transposase |
| ? | CP009273 | = 266841 | NA (NA) | coding (528/1152 nt) | insI1 | IS30 transposase | |||||
| * | ? | CP009273 | 269749 = | NA (NA) | 5 (0.060) | 5/238 | NT | NA | noncoding (1112/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 269794 = | NA (NA) | noncoding (1067/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 360104 = | 66 (0.770) | 124 (1.440) | 91/250 | NT | 65.3% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 554275 = | 74 (0.860) | 4 (0.050) | 4/238 | NT | 5.5% | intergenic (+65/‑155) | sfmA/sfmC | FimA homolog/putative periplasmic pilus chaperone |
| ? | CP009273 | 554331 = | 68 (0.830) | intergenic (+121/‑99) | sfmA/sfmC | FimA homolog/putative periplasmic pilus chaperone | |||||
| * | ? | CP009273 | = 607729 | 75 (0.870) | 4 (0.050) | 3/234 | NT | 5.1% | coding (222/2241 nt) | fepA | iron‑enterobactin outer membrane transporter |
| ? | CP009273 | = 607803 | 79 (0.980) | coding (148/2241 nt) | fepA | iron‑enterobactin outer membrane transporter | |||||
| * | ? | CP009273 | = 683437 | 5 (0.060) | 3 (0.040) | 3/246 | NT | 15.4% | noncoding (1065/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3124620 = | 28 (0.330) | intergenic (+67/+80) | insH1/yghQ | IS5 transposase and trans‑activator/putative inner membrane polysaccharide flippase | |||||
| * | ? | CP009273 | 750094 = | 90 (1.050) | 6 (0.070) | 5/246 | NT | 6.7% | intergenic (‑170/‑539) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| ? | CP009273 | 750151 = | 79 (0.930) | intergenic (‑227/‑482) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | CP009273 | = 879437 | 71 (0.820) | 4 (0.050) | 4/238 | NT | 5.5% | coding (309/1233 nt) | mdfA | multidrug efflux system protein |
| ? | CP009273 | = 879458 | 71 (0.870) | coding (330/1233 nt) | mdfA | multidrug efflux system protein | |||||
| * | ? | CP009273 | 1059209 = | 78 (0.910) | 6 (0.070) | 4/244 | NT | 7.7% | coding (23/921 nt) | cbpA | DnaK co‑chaperone; curved DNA‑binding protein |
| ? | CP009273 | 1059245 = | 67 (0.800) | intergenic (‑14/‑247) | cbpA/yccE | DnaK co‑chaperone; curved DNA‑binding protein/uncharacterized protein | |||||
| * | ? | CP009273 | 1140147 = | 71 (0.820) | 5 (0.060) | 5/238 | NT | 7.2% | coding (190/321 nt) | yceQ | uncharacterized protein |
| ? | CP009273 | 1140233 = | 62 (0.760) | coding (276/321 nt) | yceQ | uncharacterized protein | |||||
| * | ? | CP009273 | = 1164372 | 88 (1.020) | 5 (0.060) | 5/236 | NT | 6.5% | intergenic (‑84/‑157) | ycfQ/bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
| ? | CP009273 | = 1164402 | 62 (0.760) | intergenic (‑114/‑127) | ycfQ/bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein | |||||
| * | ? | CP009273 | 1203246 = | 8 (0.090) | 61 (0.810) | 52/218 | NT | 85.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 13 (0.170) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 6 (0.070) | 67 (0.890) | 53/218 | NT | 88.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 13 (0.170) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1421410 | 72 (0.840) | 6 (0.070) | 3/238 | NT | 7.7% | pseudogene (700/933 nt) | tmpR | Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein |
| ? | CP009273 | = 1421486 | 75 (0.920) | pseudogene (776/933 nt) | tmpR | Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein | |||||
| * | ? | CP009273 | 1464603 = | NA (NA) | 4 (0.050) | 4/248 | NT | 50.2% | coding (989/1152 nt) | insI1 | IS30 transposase |
| ? | CP009273 | 1464650 = | 4 (0.050) | coding (1036/1152 nt) | insI1 | IS30 transposase | |||||
| * | ? | CP009273 | 1538181 = | 51 (0.590) | 3 (0.040) | 3/246 | NT | 5.3% | coding (137/1389 nt) | narU | nitrate/nitrite transporter |
| ? | CP009273 | 1538225 = | 57 (0.670) | coding (93/1389 nt) | narU | nitrate/nitrite transporter | |||||
| * | ? | CP009273 | 1629169 = | 20 (0.230) | 3 (0.040) | 3/238 | NT | 7.3% | coding (936/963 nt) | stfQ | Qin prophage; putative side tail fiber assembly protein |
| ? | CP009273 | 1629245 = | 57 (0.700) | coding (860/963 nt) | stfQ | Qin prophage; putative side tail fiber assembly protein | |||||
| * | ? | CP009273 | 1709498 = | 76 (0.880) | 4 (0.050) | 4/240 | NT | 5.5% | coding (649/864 nt) | pdxY | pyridoxamine kinase |
| ? | CP009273 | 1709533 = | 64 (0.770) | coding (614/864 nt) | pdxY | pyridoxamine kinase | |||||
| * | ? | CP009273 | = 1735406 | 71 (0.820) | 4 (0.050) | 4/240 | NT | 5.4% | intergenic (+27/‑264) | ydhC/cfa | putative arabinose efflux transporter/cyclopropane fatty acyl phospholipid synthase (unsaturated‑phospholipid methyltransferase) |
| ? | CP009273 | = 1735442 | 71 (0.860) | intergenic (+63/‑228) | ydhC/cfa | putative arabinose efflux transporter/cyclopropane fatty acyl phospholipid synthase (unsaturated‑phospholipid methyltransferase) | |||||
| * | ? | CP009273 | = 1798509 | 69 (0.800) | 4 (0.050) | 4/240 | NT | 5.8% | pseudogene (735/1476 nt) | arpB | pseudogene, ankyrin repeats |
| ? | CP009273 | = 1798560 | 64 (0.770) | pseudogene (786/1476 nt) | arpB | pseudogene, ankyrin repeats | |||||
| * | ? | CP009273 | = 2004844 | 67 (0.780) | 4 (0.050) | 4/238 | NT | 5.6% | pseudogene (678/678 nt) | yedN | pseudogene, IpaH/YopM family |
| ? | CP009273 | = 2004919 | 71 (0.870) | pseudogene (603/678 nt) | yedN | pseudogene, IpaH/YopM family | |||||
| * | ? | CP009273 | 2031412 = | 85 (0.990) | 6 (0.070) | 4/240 | NT | 7.4% | coding (222/1359 nt) | yedV | putative sensory kinase in two‑component regulatory system with YedW |
| ? | CP009273 | 2031453 = | 68 (0.820) | coding (181/1359 nt) | yedV | putative sensory kinase in two‑component regulatory system with YedW | |||||
| * | ? | CP009273 | 2172082 = | 71 (0.820) | 5 (0.060) | 3/240 | NT | 7.2% | intergenic (‑39/‑218) | fbaB/yegT | fructose‑bisphosphate aldolase class I/nucleoside transporter, low affinity |
| ? | CP009273 | 2172121 = | 60 (0.730) | intergenic (‑78/‑179) | fbaB/yegT | fructose‑bisphosphate aldolase class I/nucleoside transporter, low affinity | |||||
| * | ? | CP009273 | 2211504 = | 78 (0.910) | 4 (0.050) | 4/242 | NT | 5.2% | coding (533/1158 nt) | yehY | inner membrane putative ABC superfamily transporter permease |
| ? | CP009273 | 2211539 = | 71 (0.850) | coding (498/1158 nt) | yehY | inner membrane putative ABC superfamily transporter permease | |||||
| * | ? | CP009273 | = 2271516 | 69 (0.800) | 4 (0.050) | 3/246 | NT | 5.4% | coding (201/345 nt) | yejG | uncharacterized protein |
| ? | CP009273 | = 2271590 | 71 (0.840) | coding (127/345 nt) | yejG | uncharacterized protein | |||||
| * | ? | CP009273 | 2549337 = | 79 (0.920) | 6 (0.070) | 4/234 | NT | 8.3% | coding (423/660 nt) | eutL | putative ethanol utilization carboxysome structural protein |
| ? | CP009273 | 2549485 = | 58 (0.720) | coding (275/660 nt) | eutL | putative ethanol utilization carboxysome structural protein | |||||
| * | ? | CP009273 | 2721769 = | NA (NA) | 6 (0.070) | 6/248 | NT | NA | noncoding (775/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | CP009273 | 2721858 = | NA (NA) | noncoding (686/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | CP009273 | 2748126 = | 76 (0.880) | 4 (0.050) | 4/236 | NT | 5.2% | intergenic (‑3/‑129) | ratA/smpB | toxic UPF0083 family protein inhibitor of 70S ribosome formation/trans‑translation protein |
| ? | CP009273 | 2748207 = | 74 (0.910) | intergenic (‑84/‑48) | ratA/smpB | toxic UPF0083 family protein inhibitor of 70S ribosome formation/trans‑translation protein | |||||
| * | ? | CP009273 | 2777852 = | 53 (0.620) | 4 (0.050) | 4/240 | NT | 6.6% | pseudogene (519/1374 nt) | ypjC | pseudogene |
| ? | CP009273 | 2777896 = | 62 (0.750) | pseudogene (475/1374 nt) | ypjC | pseudogene | |||||
| * | ? | CP009273 | 2900226 = | 61 (0.710) | 4 (0.050) | 4/240 | NT | 5.4% | coding (1075/1299 nt) | eno | enolase |
| ? | CP009273 | 2900289 = | 81 (0.980) | coding (1012/1299 nt) | eno | enolase | |||||
| * | ? | CP009273 | = 3417222 | NA (NA) | 4 (0.050) | 4/242 | NT | 40.8% | intergenic (‑76/+17) | rrfD/rrlD | 5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon |
| ? | CP009273 | 4033833 = | 6 (0.070) | intergenic (+50/‑44) | rrlA/rrfA | 23S ribosomal RNA of rrnA operon/5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 3628101 = | 80 (0.930) | 5 (0.060) | 4/234 | NT | 6.6% | intergenic (‑283/‑100) | yhiL/yhiM | pseudogene, DUF4049 family protein/acid resistance protein, inner membrane |
| ? | CP009273 | 3628166 = | 67 (0.830) | intergenic (‑348/‑35) | yhiL/yhiM | pseudogene, DUF4049 family protein/acid resistance protein, inner membrane | |||||
| * | ? | CP009273 | 3767777 = | 92 (1.070) | 5 (0.060) | 4/242 | NT | 5.4% | intergenic (+223/‑7) | mtlA/mtlD | fused mannitol‑specific PTS enzymes: IIA components/IIB components/IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent |
| ? | CP009273 | 3767796 = | 87 (1.040) | coding (13/1149 nt) | mtlD | mannitol‑1‑phosphate dehydrogenase, NAD‑dependent | |||||
| * | ? | CP009273 | 3797846 = | 60 (0.700) | 6 (0.070) | 6/240 | NT | 9.6% | coding (631/936 nt) | waaS | lipopolysaccharide core biosynthesis protein |
| ? | CP009273 | 3797885 = | 55 (0.670) | coding (592/936 nt) | waaS | lipopolysaccharide core biosynthesis protein | |||||
| * | ? | CP009273 | 3881717 = | 77 (0.890) | 4 (0.050) | 4/240 | NT | 5.3% | intergenic (+165/‑78) | mnmE/tnaC | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide |
| ? | CP009273 | 3881765 = | 69 (0.840) | intergenic (+213/‑30) | mnmE/tnaC | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase/tryptophanase leader peptide | |||||
| * | ? | CP009273 | 3939496 = | 25 (0.290) | 6 (0.070) | 3/248 | NT | 19.5% | noncoding (2433/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | CP009273 | 4033270 = | NA (NA) | noncoding (2392/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 4199811 = | 3 (0.030) | 3 (0.040) | 3/228 | NT | 32.0% | intergenic (+34/‑160) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon |
| ? | CP009273 | 4199851 = | 10 (0.130) | intergenic (+74/‑120) | gltV/rrlE | tRNA‑Glu/23S ribosomal RNA of rrnE operon | |||||
| * | ? | CP009273 | 4240518 = | 82 (0.950) | 5 (0.060) | 4/238 | NT | 6.4% | intergenic (+116/‑113) | malM/yjbI | maltose regulon periplasmic protein/pseudogene, SopA‑related, pentapeptide repeats‑containing |
| ? | CP009273 | 4240557 = | 69 (0.840) | intergenic (+155/‑74) | malM/yjbI | maltose regulon periplasmic protein/pseudogene, SopA‑related, pentapeptide repeats‑containing | |||||
| * | ? | CP009273 | 4532499 = | 70 (0.810) | 10 (0.130) | 8/232 | NT | 12.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 79 (0.990) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||