mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 47,858 | G→A | 64.0% | S30S (TCG→TCA) | kefC → | potassium:proton antiporter |
| RA | 70,434 | C→T | 62.2% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 32.4% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 44.9% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 50.0% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 51.9% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 50.9% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 59.0% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 52.4% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 30.4% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 113,035 | T→C | 17.4% | D62G (GAT→GGT) | coaE ← | dephospho‑CoA kinase |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 236,101 | A→C | 55.6% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 56.7% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 251,041 | G→A | 25.9% | A48A (GCG→GCA) | dinB → | DNA polymerase IV |
| RA | 257,873 | A→G | 53.3% | K15K (AAA→AAG) | crl → | DNA‑binding transcriptional regulator |
| RA | 267,502 | G→T | 27.8% | P228H (CCT→CAT) | ykfA ← | predicted GTP‑binding protein |
| RA | 275,785 | G→A | 50.5% | V413I (GTA→ATA) | mmuP → | predicted S‑methylmethionine transporter |
| RA | 285,498 | G→A | 38.1% | A294T (GCC→ACC) | yagG → | predicted sugar transporter |
| RA | 429,850 | T→C | 70.6% | Y8H (TAT→CAT) | yajD → | conserved hypothetical protein |
| RA | 453,395:1 | +G | 100% | intergenic (‑4/‑301) | yajG ← / → bolA | predicted lipoprotein/regulator of penicillin binding proteins and beta lactamase transcription (morphogene) |
| RA | 478,343 | C→T | 47.6% | A45T (GCT→ACT) | ylaC ← | predicted inner membrane protein |
| RA | 527,659 | A→G | 65.2% | K163E (AAA→GAA) | ylbH → | conserved hypothetical protein, rhs‑like |
| RA | 530,077 | T→C | 55.0% | Y125C (TAT→TGT) | ybbB ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 548,801 | G→A | 54.5% | pseudogene (1221/1259 nt) pseudogene (964/1002 nt) |
ylbE → ylbE → |
ECK0512:JW0508+JW0507:b4572; hypothetical protein ECK0512:JW0508:b0519; hypothetical protein, C‑ter fragment |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 620,339 | A→G | 42.9% | W25R (TGG→CGG) | fepG ← | iron‑enterobactin transporter subunit |
| RA | 639,164 | G→A | 61.9% | P63P (CCG→CCA) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 651,069 | T→C | 45.5% | N4S (AAT→AGT) | citC ← | citrate lyase synthetase |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 708,650 | C→T | 26.3% | intergenic (+471/‑106) | glnS → / → ybfM | glutamyl‑tRNA synthetase/predicted outer membrane porin |
| RA | 711,161 | C→T | 100% | intergenic (‑93/+196) | fur ← / ← fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| RA | 833,307 | G→T | 57.6% | T22T (ACC→ACA) | ybiA ← | conserved hypothetical protein |
| RA | 861,111 | G→A | 46.9% | L640L (CTG→TTG) | ybiW ← | predicted pyruvate formate lyase |
| RA | 891,153 | C→T | 61.8% | R8H (CGT→CAT) | grxA ← | glutaredoxin 1, redox coenzyme for ribonucleotide reductase (RNR1a) |
| RA | 976,718 | G→A | 34.6% | E216E (GAG→GAA) | mukE → | protein involved in chromosome partitioning |
| RA | 1,036,407 | A→G | 64.3% | E72E (GAA→GAG) | hyaD → | protein involved in processing of HyaA and HyaB proteins |
| RA | 1,074,318 | G→T | 62.5% | A39E (GCG→GAG) | ycdM ← | predicted monooxygenase |
| RA | 1,084,947 | A→G | 64.3% | K384E (AAA→GAA) | ycdB → | conserved hypothetical protein |
| RA | 1,088,483 | C→T | 73.9% | Q599Q (CAG→CAA) | ycdR ← | predicted enzyme associated with biofilm formation |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,099,547 | C→T | 61.9% | A143V (GCC→GTC) | ycdX → | predicted zinc‑binding hydrolase |
| RA | 1,115,786 | T→C | 57.1% | intergenic (‑28/+55) | msyB ← / ← mdtG | hypothetical protein/predicted drug efflux system |
| RA | 1,210,070 | C→T | 53.3% | S121F (TCC→TTC) | ymfS → | hypothetical protein |
| RA | 1,224,919 | G→A | 64.3% | intergenic (‑423/‑123) | ymgG ← / → ymgH | hypothetical protein/hypothetical protein |
| RA | 1,255,918 | C→T | 41.7% | G538S (GGC→AGC) | ycgV ← | predicted adhesin |
| RA | 1,274,854 | G→A | 58.3% | T108M (ACG→ATG) | ychN ← | conserved hypothetical protein |
| RA | 1,295,635 | T→C | 57.7% | Y178H (TAC→CAC) | tdk → | thymidine kinase/deoxyuridine kinase |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,393,837 | C→T | 59.1% | R45* (CGA→TGA) | ycjZ → | predicted DNA‑binding transcriptional regulator |
| RA | 1,413,523 | G→A | 41.7% | S47F (TCC→TTC) | ydaO ← | predicted C32 tRNA thiolase |
| RA | 1,468,907 | A→T | 18.5% | pseudogene (1802/2559 nt) pseudogene (1802/8622 nt) |
ydbA → ydbA → |
ECK1398:JW5802:b1401; predicted outer membrane protein, N‑ter fragment ECK1398:JW5802+JW1402:b4492; predicted outer membrane protein |
| RA | 1,484,463 | T→C | 44.4% | I38V (ATC→GTC) | azoR ← | NADH‑azoreductase, FMN‑dependent |
| RA | 1,559,619 | A→G | 50.0% | L45S (TTA→TCA) | ddpF ← | D‑Ala‑D‑Ala transporter subunit |
| RA | 1,584,624 | A→G | 100% | intergenic (‑386/+16) | ydeN ← / ← ydeO | conserved hypothetical protein/predicted DNA‑binding transcriptional acfivator |
| RA | 1,590,693 | A→G | 16.0% | L341L (CTT→CTC) | ydeT ← | hypothetical protein |
| RA | 1,693,796 | C→T | 52.9% | G257D (GGC→GAC) | uidC ← | predicted outer membrane porin protein |
| RA | 1,721,565 | T→C | 25.0% | intergenic (‑249/‑25) | ydhH ← / → slyB | conserved hypothetical protein/outer membrane lipoprotein |
| RA | 1,857,513 | C→T | 29.0% | G58E (GGA→GAA) | ydjG ← | predicted oxidoreductase |
| RA | 1,872,074 | T→C | 16.0% | intergenic (+122/‑25) | yeaH → / → yeaI | conserved hypothetical protein/predicted diguanylate cyclase |
| RA | 2,176,396 | C→T | 72.4% | M6I (ATG→ATA) | gatC ← | galactitol‑specific enzyme IIC component of PTS |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,218,928 | T→C | 29.6% | I243I (ATT→ATC) | mlrA → | DNA‑binding transcriptional regulator |
| RA | 2,238,432 | T→C | 100% | L356L (TTA→CTA) | yeiT → | predicted oxidoreductase |
| RA | 2,266,989 | T→C | 52.2% | intergenic (‑160/‑208) | fruB ← / → setB | fused fructose‑specific PTS enzyme IIA component and HPr component/lactose/glucose efflux system |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,358,400 | G→A | 57.1% | A362T (GCT→ACT) | glpA → | sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding |
| RA | 2,389,320 | T→C | 16.7% | N358S (AAC→AGC) | yfbK ← | conserved hypothetical protein |
| RA | 2,433,800 | G→A | 16.7% | T91T (ACC→ACT) | ubiX ← | 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase |
| RA | 2,462,102 | A→G | 42.9% | F53L (TTC→CTC) | sixA ← | phosphohistidine phosphatase |
| RA | 2,792,695 | C→T | 66.7% | intergenic (+24/‑214) | gabT → / → gabP | 4‑aminobutyrate aminotransferase, PLP‑dependent/gamma‑aminobutyrate transporter |
| RA | 2,809,581 | G→A | 61.5% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,841,531 | G→A | 40.9% | R57* (CGA→TGA) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,966,215 | T→G | 56.6% | K292N (AAA→AAC) | ptsP ← | fused PEP‑protein phosphotransferase (enzyme I) of PTS system |
| RA | 3,001,511 | T→C | 54.8% | I81T (ATA→ACA) | xdhB → | xanthine dehydrogenase, FAD‑binding subunit |
| RA | 3,054,203 | G→A | 22.2% | intergenic (‑103/‑65) | ygfB ← / → zapA | hypothetical protein/protein that localizes to the cytokinetic ring |
| RA | 3,139,938 | C→T | 41.7% | R2H (CGT→CAT) | hybD ← | predicted maturation element for hydrogenase 2 |
| RA | 3,213,568 | C→T | 52.9% | intergenic (+24/+55) | rpoD → / ← ygjF | RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase |
| RA | 3,220,824 | C→A | 33.3% | P235T (CCG→ACG) | ebgR → | DNA‑binding transcriptional repressor |
| RA | 3,224,816 | C→T | 43.3% | H147Y (CAT→TAT) | ebgC → | cryptic beta‑D‑galactosidase, beta subunit |
| RA | 3,233,407 | T→C | 12.9% | G375G (GGA→GGG) | ygjO ← | predicted methyltransferase small domain |
| RA | 3,244,017 | G→A | 46.9% | Q86Q (CAG→CAA) | exuT → | hexuronate transporter |
| RA | 3,249,944 | C→A | 21.6% | P89T (CCG→ACG) | yqjG → | predicted S‑transferase |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,294,438 | T→C | 55.6% | L395S (TTG→TCG) | yraM → | conserved hypothetical protein |
| RA | 3,306,434 | G→A | 27.8% | L428L (CTG→TTG) | deaD ← | ATP‑dependent RNA helicase |
| RA | 3,332,615 | T→A | 52.7% | intergenic (‑25/+102) | yhbE ← / ← rpmA | conserved inner membrane protein/50S ribosomal subunit protein L27 |
| RA | 3,338,549 | G→A | 45.0% | F185F (TTC→TTT) | yrbE ← | predicted toluene transporter subunit |
| RA | 3,353,829 | G→A | 12.9% | T26M (ACG→ATG) | yhcC ← | predicted Fe‑S oxidoreductase |
| RA | 3,363,041 | T→C | 15.4% | L127S (TTA→TCA) | yhcD → | predicted outer membrane protein |
| RA | 3,459,280 | T→C | 60.0% | E15G (GAA→GGA) | secE ← | preprotein translocase membrane subunit |
| RA | 3,532,412 | T→C | 40.0% | M236T (ATG→ACG) | cpxA → | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 3,584,576 | G→A | 68.7% | P21S (CCA→TCA) | hemN ← | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| RA | 3,615,349 | A→G | 23.8% | P369P (CCT→CCC) | ubiB ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,639,730 | T→C | 41.7% | K222R (AAA→AGA) | xerC ← | site‑specific tyrosine recombinase |
| RA | 3,657,262 | C→T | 50.0% | E273E (GAG→GAA) | wzyE ← | predicted Wzy protein involved in ECA polysaccharide chain elongation |
| RA | 3,704,876 | C→T | 57.1% | M164I (ATG→ATA) | trkD ← | potassium transporter |
| RA | 3,707,036 | G→A | 44.4% | A483T (GCC→ACC) | yieN → | fused predicted transcriptional regulators |
| RA | 3,727,747 | T→C | 38.9% | V168V (GTT→GTC) | pstA → | phosphate transporter subunit |
| RA | 3,735,429 | G→A | 31.4% | A323T (GCA→ACA) | bglH → | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,739,327 | C→T | 51.4% | V195I (GTT→ATT) | yieH ← | predicted hydrolase |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | 100% | insH | insH | |
| RA | 3,783,789 | C→A | 28.5% | D72Y (GAC→TAC) | yidI ← | predicted inner membrane protein |
| RA | 3,806,473 | G→A | 47.1% | P198P (CCG→CCA) | yicI → | predicted alpha‑glucosidase |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,915,241 | A→G | 57.9% | E48G (GAG→GGG) | glyQ → | glycine tRNA synthetase, alpha subunit |
| RA | 3,986,216 | A→G | 13.3% | Y81H (TAT→CAT) | slp ← | outer membrane lipoprotein |
| RA | 4,012,376 | G→A | 56.5% | A500T (GCC→ACC) | rbbA → | fused ribosome‑associated ATPases |
| RA | 4,017,703 | T→C | 58.8% | N1175D (AAC→GAC) | rhsB ← | rhsB element core protein RshB |
| RA | 4,036,723 | G→A | 100% | A184T (GCT→ACT) | ftsY → | fused Signal Recognition Particle (SRP) receptor |
| RA | 4,083,312 | G→A | 45.5% | G325E (GGG→GAG) | rtcB → | conserved hypothetical protein |
| RA | 4,123,875 | G→A | 43.7% | R255H (CGC→CAC) | damX → | hypothetical protein |
| RA | 4,125,004 | A→T | 7.7% | D167V (GAT→GTT) | dam → | DNA adenine methylase |
| RA | 4,173,819 | G→A | 17.4% | V43M (GTG→ATG) | bfr → | bacterioferritin, iron storage and detoxification protein |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,333,478 | G→A | 54.5% | R555H (CGC→CAC) | yjdA → | conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
| RA | 4,350,232 | G→A | 52.0% | R3C (CGC→TGC) | yjdF ← | conserved inner membrane protein |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,392,090 | G→T | 43.7% | L655M (CTG→ATG) | yjeP ← | predicted mechanosensitive channel |
| RA | 4,407,692 | C→T | 100% | R325C (CGT→TGT) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 4,443,410 | G→A | 40.0% | L179L (CTG→TTG) | ytfJ ← | predicted transcriptional regulator |
| RA | 4,477,260 | G→A | 54.1% | intergenic (‑45/+236) | pyrL ← / ← yjgH | pyrBI operon leader peptide/predicted mRNA endoribonuclease |
| RA | 4,480,143 | T→C | 21.9% | Y9H (TAT→CAT) | yjgL → | hypothetical protein |
| RA | 4,561,090 | G→A | 55.6% | intergenic (‑88/‑585) | yjiC ← / → yjiD | hypothetical protein/DNA replication/recombination/repair protein |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,580,803 | C→T | 55.6% | pseudogene (1987/2721 nt) | yjiV → | ECK4334:JW5954:b4486; conserved hypothetical protein |
| RA | 4,583,739 | A→G | 12.5% | F94S (TTC→TCC) | mcrB ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB |
| RA | 4,586,637 | G→A | 72.2% | P365L (CCG→CTG) | hsdM ← | DNA methylase M |
| RA | 4,588,402 | C→T | 52.0% | L1032L (CTG→CTA) | hsdR ← | endonuclease R |
| RA | 4,591,445 | G→A | 42.1% | T18I (ACA→ATA) | hsdR ← | endonuclease R |
| RA | 4,604,824 | G→A | 57.1% | S16S (AGC→AGT) | yjjA ← | conserved hypothetical protein |
| RA | 4,632,877 | A→G | 37.5% | Y294C (TAC→TGC) | nadR → | bifunctional DNA‑binding transcriptional repressor and NMN adenylyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 171671 | 171697 | 27 | 2 [1] | [1] 2 | fhuB | fused subunits of iron‑hydroxamate transporter and membrane components of ABC superfamily transporter |
| * | * | ÷ | W3110S.gb | 276224 | 276255 | 32 | 2 [1] | [1] 2 | mmuM | S‑methylmethionine:homocysteine methyltransferase |
| * | * | ÷ | W3110S.gb | 283104 | 283122 | 19 | 2 [1] | [1] 2 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 287639 | 287718 | 80 | 2 [1] | [1] 2 | yagI | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 397834 | 397849 | 16 | 2 [1] | [0] 4 | yaiW | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 422765 | 422794 | 30 | 3 [1] | [1] 2 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573866–575007 | 575999 | 993–2134 | 2 [0] | [0] 55 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 598770 | 598804 | 35 | 2 [1] | [1] 2 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 721525 | 721545 | 21 | 2 [1] | [1] 3 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 730182 | 730200 | 19 | 4 [1] | [1] 2 | rhsC | rhsC element core protein RshC |
| * | * | ÷ | W3110S.gb | 907995 | 908022 | 28 | 2 [1] | [1] 2 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 1081342 | 1081368 | 27 | 2 [1] | [1] 2 | putP/ycdN | proline:sodium symporter/ECK1007:JW5141:b1016; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1173211 | 1173211 | 1 | 2 [0] | [0] 2 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1184598 | 1184624 | 27 | 3 [1] | [1] 2 | potC | polyamine transporter subunit |
| * | * | ÷ | W3110S.gb | 1322301 | 1322315 | 15 | 2 [1] | [1] 2 | trpD | fused glutamine amidotransferase (component II) of anthranilate synthase and anthranilate phosphoribosyl transferase |
| * | * | ÷ | W3110S.gb | 1328331 | 1328354 | 24 | 2 [1] | [1] 2 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1338222 | 1338232 | 11 | 2 [1] | [1] 3 | acnA | aconitate hydratase 1 |
| * | * | ÷ | W3110S.gb | 1421310 | 1421334 | 25 | 3 [1] | [0] 2 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1423355 | 1423389 | 35 | 2 [0] | [1] 2 | ydaU | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1888538 | 1888576 | 39 | 2 [1] | [1] 2 | yeaX/rnd | predicted oxidoreductase/ribonuclease D |
| * | * | ÷ | W3110S.gb | 2296381 | 2296395 | 15 | 2 [1] | [1] 2 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2536306 | 2536326 | 21 | 3 [1] | [1] 2 | zipA | cell division protein involved in Z ring assembly |
| * | * | ÷ | W3110S.gb | 2569097 | 2569132 | 36 | 2 [1] | [1] 2 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2777816 | 2777826 | 11 | 5 [1] | [1] 3 | ypjA | adhesin‑like autotransporter |
| * | * | ÷ | W3110S.gb | 2790468 | 2790508 | 41 | 2 [1] | [1] 2 | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| * | * | ÷ | W3110S.gb | 2827389 | 2827419 | 31 | 2 [1] | [1] 3 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 2876569 | 2876610 | 42 | 2 [0] | [1] 2 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |
| * | * | ÷ | W3110S.gb | 2876709 | 2876735 | 27 | 2 [1] | [1] 2 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |
| * | * | ÷ | W3110S.gb | 3799043 | 3799054 | 12 | 3 [1] | [1] 2 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 4326167 | 4326195 | 29 | 2 [1] | [1] 2 | phnG | carbon‑phosphorus lyase complex subunit |
| * | * | ÷ | W3110S.gb | 4344050 | 4344062 | 13 | 2 [1] | [1] 2 | adiA | biodegradative arginine decarboxylase |
| * | * | ÷ | W3110S.gb | 4601184 | 4601192 | 9 | 2 [0] | [1] 2 | yjjN | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 21 (1.130) | 30 (2.070) +CGCGTACAACT |
23/78 | NT | 66.4% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 18 (0.970) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 21 (1.130) | 14/100 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 10 (0.540) | 25 (1.430) +TCA |
19/94 | NT | 84.2% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 19 (1.020) | 15/100 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 24 (1.290) | 18/100 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 713380 = | 24 (1.290) | 21 (1.230) | 15/92 | NT | 53.8% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 14 (0.820) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 22 (1.180) | 25 (1.340) | 22/100 | NT | 50.5% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 27 (1.450) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 13 (0.700) | 14 (1.110) | 10/68 | NT | 68.6% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 4 (0.320) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 1 (0.050) | 17 (0.970) | 16/94 | NT | 94.8% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 2 (0.110) | 12 (0.670) | 10/96 | NT | 86.2% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | 2172309 = | NA (NA) | 17 (0.950) | 14/96 | NT | 100% | pseudogene (1562/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 36 (1.970) | 26/98 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 12 (0.640) | 11/100 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 32 (1.720) | 23/100 | NT | 84.2% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 6 (0.320) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | = 2855747 | 22 (1.180) | 8 (0.440) | 5/98 | NT | 32.3% | intergenic (‑285/‑2) | ygbA/mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| ? | W3110S.gb | 4124505 = | 12 (0.660) | coding (1/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | 3748799 = | 4 (0.210) | 16 (0.860) | 14/100 | NT | 80.0% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 4547364 = | 5 (0.270) | 9 (0.590) | 6/82 | NT | 59.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 8 (0.520) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 5 (0.270) | 10 (0.660) | 7/82 | NT | 62.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 8 (0.520) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||