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 | 15,286 | C→T | 100% | D373D (GAC→GAT) | dnaJ → | chaperone Hsp40, co‑chaperone with DnaK |
| RA | 45,813 | C→T | 100% | P3S (CCG→TCG) | yaaU → | predicted transporter |
| RA | 47,828 | A→G | 85.5% | V20V (GTA→GTG) | kefC → | potassium:proton antiporter |
| RA | 65,135 | C→T | 100% | D216N (GAT→AAT) | polB ← | DNA polymerase II |
| RA | 70,244 | T→C | 15.5% | intergenic (‑196/‑143) | araB ← / → araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| RA | 70,434 | C→T | 61.5% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 69.7% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 76.8% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 72.7% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 72.8% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 70.4% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 75.2% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 70.9% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 77.1% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 85,966 | T→C | 61.9% | F113L (TTT→CTT) | ilvI → | acetolactate synthase III, large subunit |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 230,040 | C→A | 100% | R281L (CGC→CTC) | yafC ← | predicted DNA‑binding transcriptional regulator |
| RA | 234,234 | C→T | 78.8% | L183L (TTG→TTA) | gloB ← | predicted hydroxyacylglutathione hydrolase |
| RA | 236,101 | A→C | 75.5% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 73.2% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 249,599 | A→G | 31.0% | pseudogene (472/1713 nt) | fhiA ← | ECK0230:JW5811:b0229; flagellar system protein, promoterless fragment |
| RA | 344,381 | G→A | 100% | intergenic (+166/‑247) | yahL → / → yahM | hypothetical protein/hypothetical protein |
| RA | 381,851 | A→C | 77.8% | G88G (GGT→GGG) | yaiF ← | hypothetical protein |
| RA | 393,168 | T→C | 82.4% | G310G (GGT→GGC) | yaiU → | hypothetical protein |
| RA | 494,006 | T→A | 9.1% | D126E (GAT→GAA) | recR → | gap repair protein |
| RA | 496,170 | A→G | 100% | E609E (GAA→GAG) | htpG → | molecular chaperone HSP90 family |
| RA | 515,934 | C→T | 82.0% | A43V (GCG→GTG) | ybbM → | predicted inner membrane protein |
| RA | 531,446 | C→T | 56.1% | intergenic (‑1/‑229) | ybbS ← / → allA | transcriptional activator of the allD operon/ureidoglycolate hydrolase |
| 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 | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 579,680 | G→A | 100% | intergenic (+371/‑377) | ybcW → / → nohB | hypothetical protein/DNA packaging protein |
| RA | 579,794 | A→G | 59.3% | intergenic (+485/‑263) | ybcW → / → nohB | hypothetical protein/DNA packaging protein |
| RA | 588,045 | A→G | 72.4% | D711D (GAT→GAC) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| RA | 614,426 | C→T | 76.6% | L349L (CTC→CTT) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 669,029 | C→T | 51.4% | E37K (GAA→AAA) | ybeA ← | conserved hypothetical protein |
| RA | 810,589 | T→G | 100% | M275R (ATG→AGG) | bioB → | biotin synthase |
| RA | 827,597 | C→T | 100% | P26P (CCG→CCA) | ybhS ← | predicted transporter subunit |
| RA | 904,996 | G→A | 84.0% | intergenic (‑107/‑19) | ybjP ← / → ybjQ | predicted lipoprotein/conserved hypothetical protein |
| RA | 906,962 | G→A | 100% | H72Y (CAC→TAC) | ybjS ← | predicted NAD(P)H oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 913,779 | A→G | 79.0% | L153P (CTG→CCG) | hcp ← | hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases |
| RA | 941,935 | C→T | 100% | T185T (ACC→ACT) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 978,430 | A→G | 100% | E561E (GAA→GAG) | mukB → | fused chromosome partitioning proteins |
| RA | 1,016,291 | T→C | 100% | V52A (GTA→GCA) | rmf → | ribosome modulation factor |
| RA | 1,020,867 | A→G | 100% | S159P (TCC→CCC) | sulA ← | SOS cell division inhibitor |
| RA | 1,056,565 | G→A | 50.0% | G12G (GGC→GGT) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,068,568 | T→A | 12.2% | G22G (GGT→GGA) | ymdF → | conserved hypothetical protein |
| RA | 1,075,828 | T→C | 66.7% | L1159L (TTA→TTG) | putA ← | fused DNA‑binding transcriptional regulator, proline dehydrogenase, and pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,109,964 | G→A | 100% | C185C (TGC→TGT) | mdoC ← | membrane protein required for modification of periplasmic glucan |
| RA | 1,172,268 | T→C | 100% | K1092E (AAG→GAG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,173,170 | C→T | 100% | R791H (CGT→CAT) | mfd ← | transcription‑repair coupling factor |
| RA | 1,175,236 | C→A | 100% | Q102H (CAG→CAT) | mfd ← | transcription‑repair coupling factor |
| RA | 1,181,288 | T→G | 100% | D64E (GAT→GAG) | cobB → | deacetylase of acetyl‑CoA synthetase, NAD‑dependent |
| RA | 1,185,915 | A→G | 48.8% | M36T (ATG→ACG) | potB ← | polyamine transporter subunit |
| RA | 1,203,986 | G→A | 6.3% | F175F (TTC→TTT) | ymfK ← | repressor protein phage e14 |
| RA | 1,244,320 | C→T | 100% | C113Y (TGC→TAC) | ldcA ← | L,D‑carboxypeptidase A |
| 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 | 1,339,708 | G→A | 100% | A722T (GCC→ACC) | acnA → | aconitate hydratase 1 |
| RA | 1,373,368 | G→A | 86.3% | R480H (CGT→CAT) | ycjM → | predicted glucosyltransferase |
| RA | 1,376,428 | G→A | 100% | V209M (GTG→ATG) | ycjP → | predicted sugar transporter subunit |
| RA | 1,426,674 | T→C | 83.8% | D393D (GAT→GAC) | trkG → | potassium transporter subunit |
| RA | 1,441,198 | G→A | 17.4% | T434I (ACC→ATC) | ydbK ← | fused predicted Fe‑S subunit of pyruvate‑flavodoxin oxidoreductase |
| RA | 1,463,502 | C→T | 100% | P299L (CCG→CTG) | paaJ → | predicted beta‑ketoadipyl CoA thiolase |
| RA | 1,477,935 | G→A | 73.6% | E360K (GAA→AAA) | ydbD → | hypothetical protein |
| RA | 1,495,966:1 | +T | 100% | coding (820/924 nt) | ydcI ← | predicted DNA‑binding transcriptional regulator |
| RA | 1,521,063 | C→T | 100% | S108F (TCC→TTC) | yncB → | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| RA | 1,547,470 | C→T | 75.3% | S91S (TCG→TCA) | yddL ← | predicted lipoprotein |
| RA | 1,569,965 | T→C | 100% | Q191Q (CAA→CAG) | yddW ← | predicted liprotein |
| RA | 1,581,839 | C→T | 100% | M222I (ATG→ATA) | ydeM ← | conserved hypothetical protein |
| RA | 1,588,010 | T→G | 100% | D64A (GAC→GCC) | ydeP ← | predicted oxidoreductase |
| RA | 1,595,724 | G→A | 72.7% | pseudogene (56/1401 nt) | ydeU ← | ECK1502:JW1502:b1509; conserved hypothetical protein |
| RA | 1,606,841 | C→T | 68.5% | A26V (GCC→GTC) | lsrB → | AI2 transporter |
| RA | 1,618,668 | A→G | 6.9% | intergenic (+76/‑74) | yneK → / → ydeA | hypothetical protein/predicted arabinose transporter |
| RA | 1,620,710 | C→T | 87.3% | intergenic (‑88/‑124) | marC ← / → marR | predicted transporter/DNA‑binding transcriptional repressor |
| RA | 1,657,562 | T→C | 100% | I14T (ATT→ACT) | ynfB → | hypothetical protein |
| RA | 1,682,586 | A→G | 68.0% | Q439R (CAG→CGG) | ydgI → | predicted arginine/ornithine antiporter transporter |
| RA | 1,692,839 | G→A | 67.9% | G425D (GGT→GAT) | ydgA → | conserved hypothetical protein |
| RA | 1,742,822 | A→G | 80.4% | S400G (AGC→GGC) | ydhC → | predicted transporter |
| RA | 1,761,776 | C→T | 100% | L154L (CTG→CTA) | sufS ← | selenocysteine lyase, PLP‑dependent |
| RA | 1,775,080 | T→C | 62.9% | F285F (TTT→TTC) | ydiN → | predicted transporter |
| RA | 1,846,634 | Δ1 bp | 100% | intergenic (‑49/+79) | ynjI ← / ← topB | predicted inner membrane protein/DNA topoisomerase III |
| RA | 1,887,874 | T→C | 100% | F106L (TTT→CTT) | yeaX → | predicted oxidoreductase |
| RA | 1,927,287 | T→C | 100% | L45P (CTT→CCT) | yobB → | conserved hypothetical protein |
| RA | 1,965,064 | G→A | 100% | I567I (ATC→ATT) | flhA ← | predicted flagellar export pore protein |
| RA | 1,995,272 | T→C | 100% | S524S (TCA→TCG) | uvrC ← | excinuclease UvrABC, endonuclease subunit |
| RA | 1,998,457 | T→C | 6.5% | E171E (GAA→GAG) | sdiA ← | DNA‑binding transcriptional activator |
| RA | 1,999,934 | A→G | 47.4% | V6V (GTT→GTC) | yecC ← | predicted transporter subunit |
| RA | 2,035,868:1 | +T | 100% | intergenic (‑247/‑320) | yedR ← / → yedS | predicted inner membrane protein/ECK1962:JW5319:b1964; hypothetical protein, N‑ter fragment |
| RA | 2,077,980 | C→T | 100% | Y355Y (TAC→TAT) | yeeR → | predicted membrane protein |
| RA | 2,085,271 | A→G | 46.1% | S127G (AGC→GGC) | sbcB → | exonuclease I |
| RA | 2,129,117 | C→T | 45.2% | A71T (GCC→ACC) | fcl ← | bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase and GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase |
| RA | 2,160,543 | C→T | 100% | F7F (TTC→TTT) | mdtC → | multidrug efflux system, subunit C |
| RA | 2,169,960:1 | +T | 100% | intergenic (‑3/+166) | yegZ ← / ← yegR | ECK2080:JW5886:b2083; hypothetical protein fragment/hypothetical protein |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,193,388 | T→C | 7.1% | Q286R (CAG→CGG) | yehB ← | predicted outer membrane protein |
| RA | 2,198,825 | G→A | 100% | A398T (GCG→ACG) | metG → | methionyl‑tRNA synthetase |
| RA | 2,295,693 | C→T | 8.5% | A18T (GCG→ACG) | ccmH ← | heme lyase, CcmH subunit |
| RA | 2,313,823 | T→C | 76.8% | E349G (GAA→GGA) | yojL ← | predicted thiamine biosynthesis lipoprotein |
| RA | 2,315,568 | A→G | 100% | G172G (GGT→GGC) | ompC ← | outer membrane porin protein C |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,328,254 | C→T | 14.3% | D46D (GAC→GAT) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| RA | 2,350,543 | G→A | 100% | V337I (GTA→ATA) | nrdA → | ribonucleoside diphosphate reductase 1, alpha subunit |
| RA | 2,381,930 | Δ1 bp | 100% | coding (333/759 nt) | yfbB ← | predicted peptidase |
| RA | 2,397,191 | A→G | 78.3% | F174S (TTC→TCC) | nuoM ← | NADH:ubiquinone oxidoreductase, membrane subunit M |
| RA | 2,427,890 | T→G | 100% | I246S (ATT→AGT) | yfcH → | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,428,249 | A→G | 14.6% | I246T (ATT→ACT) | yfcI ← | conserved hypothetical protein |
| RA | 2,501,495 | G→A | 100% | S135S (TCG→TCA) | ddg → | palmitoleoyl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 2,512,230 | A→G | 16.1% | W371R (TGG→CGG) | ypdG ← | predicted enzyme IIC component of PTS |
| RA | 2,512,687 | Δ1 bp | 100% | coding (654/1248 nt) | ypdG ← | predicted enzyme IIC component of PTS |
| RA | 2,541,664 | G→A | 87.2% | E129K (GAA→AAA) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,552,318 | T→C | 63.2% | F67S (TTT→TCT) | murP → | fused predicted enzyme IIBC components of PTS |
| RA | 2,589,664 | A→T | 80.3% | intergenic (+300/‑239) | acrD → / → yffB | aminoglycoside/multidrug efflux system/conserved hypothetical protein |
| RA | 2,594,104 | G→A | 100% | H138Y (CAT→TAT) | ypfI ← | predicted hydrolase |
| RA | 2,599,304 | G→A | 100% | M57I (ATG→ATA) | bcp → | thiol peroxidase, thioredoxin‑dependent |
| RA | 2,636,526 | C→T | 100% | L261L (CTG→CTA) | yfgL ← | protein assembly complex, lipoprotein component |
| RA | 2,667,558 | T→C | 100% | intergenic (‑6/‑130) | hcaR ← / → hcaE | DNA‑binding transcriptional regulator/3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,669,838 | T→C | 75.0% | V92A (GTT→GCT) | hcaC → | 3‑phenylpropionate dioxygenase, predicted ferredoxin subunit |
| RA | 2,688,036 | T→C | 71.8% | I43V (ATT→GTT) | yfhG ← | conserved hypothetical protein |
| RA | 2,697,845 | G→A | 100% | G144D (GGT→GAT) | yfhH → | predicted DNA‑binding transcriptional regulator |
| RA | 2,702,790 | C→T | 73.4% | intergenic (‑71/+201) | rnc ← / ← lepB | RNase III/leader peptidase |
| RA | 2,706,728 | G→A | 64.1% | P228L (CCA→CTA) | rseB ← | anti‑sigma factor |
| RA | 2,717,229 | G→A | 100% | intergenic (‑45/‑162) | yfiF ← / → trxC | predicted methyltransferase/thioredoxin 2 |
| RA | 2,759,336 | C→T | 92.0% | T45I (ACA→ATA) | yfjJ → | hypothetical protein |
| RA | 2,773,435 | T→C | 78.7% | L488L (TTG→CTG) | yfjW → | predicted inner membrane protein |
| RA | 2,777,419:1 | +A | 100% | coding (3964/4581 nt) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,794,102 | G→A | 100% | L398L (TTG→TTA) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,809,581 | G→A | 76.9% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,821,480 | T→C | 76.0% | T316A (ACC→GCC) | recA ← | DNA strand exchange and recombination protein with protease and nuclease activity |
| RA | 2,821,628 | G→A | 57.7% | G266G (GGC→GGT) | recA ← | DNA strand exchange and recombination protein with protease and nuclease activity |
| RA | 2,840,761 | A→G | 89.8% | E372E (GAA→GAG) | ascB → | cryptic 6‑phospho‑beta‑glucosidase |
| RA | 2,841,727 | C→T | 77.2% | A126T (GCC→ACC) | hycH ← | protein required for maturation of hydrogenase 3 |
| RA | 2,860,110 | G→A | 80.0% | V9I (GTC→ATC) | ygbJ → | predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,867,123 | G→A | 100% | P96L (CCG→CTG) | nlpD ← | predicted outer membrane lipoprotein |
| RA | 2,885,984 | C→T | 75.0% | intergenic (‑109/+250) | ygcB ← / ← cysH | conserved hypothetical protein, member of DEAD box family/3'‑phosphoadenosine 5'‑phosphosulfate reductase |
| RA | 2,910,539 | C→A | 100% | R590L (CGC→CTC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,916,386 | G→A | 100% | E892K (GAA→AAA) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,931,037 | C→A | 71.5% | A212A (GCG→GCT) | fucO ← | L‑1,2‑propanediol oxidoreductase |
| RA | 2,938,519 | A→G | 70.4% | I166V (ATC→GTC) | fucR → | DNA‑binding transcriptional activator |
| RA | 3,002,965 | A→G | 8.3% | L493S (TTA→TCA) | ygeV ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,013,681 | G→A | 79.7% | V11V (GTC→GTT) | yqeC ← | conserved hypothetical protein |
| RA | 3,061,031 | A→G | 100% | Q509R (CAG→CGG) | yliK → | methylmalonyl‑CoA mutase |
| RA | 3,079,041 | A→G | 100% | I417I (ATT→ATC) | tktA ← | transketolase 1, thiamin‑binding |
| RA | 3,135,166 | A→G | 81.1% | intergenic (‑139/+153) | pitB ← / ← gss | phosphate transporter/fused glutathionylspermidine amidase and glutathionylspermidine synthetase |
| RA | 3,164,775 | C→T | 63.2% | A534T (GCA→ACA) | ygiS ← | predicted transporter subunit |
| RA | 3,194,164 | T→C | 100% | T416A (ACG→GCG) | rfaE ← | fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| RA | 3,205,103 | A→G | 100% | intergenic (‑191/‑16) | ygiP ← / → ttdA | predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit |
| RA | 3,225,032 | Δ1 bp | 100% | coding (143/1434 nt) | ygjI → | predicted transporter |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,349,295 | C→T | 61.8% | A124T (GCC→ACC) | mtgA ← | biosynthetic peptidoglycan transglycosylase |
| RA | 3,358,271 | A→G | 100% | K1262R (AAA→AGA) | gltB → | glutamate synthase, large subunit |
| RA | 3,364,443 | T→C | 12.1% | L594L (CTT→CTC) | yhcD → | predicted outer membrane protein |
| RA | 3,365,218 | A→G | 63.4% | pseudogene (179/480 nt) pseudogene (179/1745 nt) |
yhcE → yhcE → |
ECK3207:JW3184:b3217; hypothetical protein, N‑ter fragment ECK3207:JW3184+JW3187:b4569; hypothetical protein |
| RA | 3,381,341 | T→C | 9.3% | S248S (AGT→AGC) | degQ → | serine endoprotease, periplasmic |
| RA | 3,404,820 | G→A | 73.5% | intergenic (+507/‑471) | yhdH → / → accB | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit |
| RA | 3,447,843 | A→G | 76.5% | V1163V (GTT→GTC) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 3,566,303 | T→C | 77.2% | C8C (TGT→TGC) | yihR → | predicted aldose‑1‑epimerase |
| RA | 3,573,836 | A→G | 90.3% | V200A (GTG→GCG) | yihN ← | predicted transporter |
| RA | 3,587,198 | C→T | 100% | E840K (GAA→AAA) | polA ← | fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
| RA | 3,622,543 | C→T | 53.3% | A362A (GCG→GCA) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 3,679,440 | A→G | 80.6% | I194V (ATT→GTT) | ilvY → | DNA‑binding transcriptional dual regulator |
| RA | 3,682,573 | G→A | 100% | L211L (CTG→TTG) | ilvD ← | dihydroxyacid dehydratase |
| RA | 3,705,799 | A→G | 100% | E70E (GAA→GAG) | yieN → | fused predicted transcriptional regulators |
| RA | 3,709,115 | C→T | 16.0% | E138E (GAG→GAA) | asnA ← | asparagine synthetase A |
| 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 | 3,780,496 | G→A | 76.6% | G66R (GGG→AGG) | yidK → | predicted transporter |
| RA | 3,792,107 | Δ1 bp | 100% | coding (315/1320 nt) | uhpC → | membrane protein regulates uhpT expression |
| RA | 3,815,914 | T→C | 76.7% | N702D (AAT→GAT) | spoT ← | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| 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 | 3,861,751 | T→C | 78.3% | N423S (AAC→AGC) | lldP ← | L‑lactate permease |
| RA | 3,934,836 | T→C | 11.9% | I70I (ATT→ATC) | dppB → | dipeptide transporter |
| RA | 4,008,583 | C→T | 67.1% | Q253* (CAA→TAA) | yhiJ → | hypothetical protein |
| RA | 4,066,786 | C→T | 100% | intergenic (+144/‑129) | asd → / → glgB | aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding/1,4‑alpha‑glucan branching enzyme |
| RA | 4,071,419:1 | +A | 100% | coding (331/1296 nt) | glgC → | glucose‑1‑phosphate adenylyltransferase |
| RA | 4,124,493 | T→C | 57.1% | intergenic (+95/‑12) | damX → / → dam | hypothetical protein/DNA adenine methylase |
| RA | 4,154,666 | A→G | 100% | I23V (ATT→GTT) | yhfA → | conserved hypothetical protein |
| RA | 4,155,146:1 | +A | 60.6% | coding (783/870 nt) | prkB ← | predicted phosphoribulokinase |
| RA | 4,177,469 | G→A | 100% | A9V (GCG→GTG) | gspK ← | general secretory pathway component, cryptic |
| RA | 4,246,866 | T→C | 31.4% | V81V (GTA→GTG) | malG ← | maltose transporter subunit |
| RA | 4,271,811 | A→G | 87.9% | Y369C (TAT→TGT) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,295,565 | T→C | 100% | F154F (TTT→TTC) | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,378,355 | T→C | 66.7% | K188E (AAA→GAA) | yjeJ ← | hypothetical protein |
| RA | 4,428,262:1 | +G | 100% | coding (735/855 nt) | ulaE → | L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 4,486,264 | C→T | 100% | P752P (CCG→CCA) | valS ← | valyl‑tRNA synthetase |
| RA | 4,491,067 | G→A | 68.1% | V56V (GTG→GTA) | yjgP → | conserved inner membrane protein |
| RA | 4,501,102 | T→C | 69.1% | noncoding (16/85 nt) | leuX → | tRNA‑Leu |
| RA | 4,501,500 | A→G | 100% | Q23Q (CAA→CAG) | intB → | predicted integrase |
| RA | 4,501,608 | A→G | 100% | K59K (AAA→AAG) | intB → | predicted integrase |
| RA | 4,528,968 | A→G | 74.5% | L242P (CTA→CCA) | yjhH ← | predicted lyase/synthase |
| RA | 4,547,549 | T→C | 13.8% | intergenic (+234/‑248) | fimE → / → fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| RA | 4,549,768 | C→T | 75.9% | intergenic (+57/‑10) | fimC → / → fimD | chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,629,902 | C→T | 100% | T109M (ACG→ATG) | serB → | 3‑phosphoserine phosphatase |
| RA | 4,640,981 | C→T | 30.0% | A98V (GCT→GTT) | creB → | DNA‑binding response regulator in two‑component regulatory system with CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 171668 | 171690 | 23 | 5 [3] | [2] 5 | fhuB | fused subunits of iron‑hydroxamate transporter and membrane components of ABC superfamily transporter |
| * | * | ÷ | W3110S.gb | 422758 | 422797 | 40 | 7 [3] | [3] 4 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573871–575008 | 575999 | 992–2129 | 4 [3] | [0] 92 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721521 | 721545 | 25 | 5 [3] | [1] 9 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 907994 | 908008 | 15 | 5 [2] | [1] 5 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 915574 | 915647 | 74 | 4 [3] | [2] 6 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 1041895 | 1041911 | 17 | 7 [0] | [2] 5 | appA | phosphoanhydride phosphorylase |
| * | * | ÷ | W3110S.gb | 1173200 | 1173218 | 19 | 4 [3] | [0] 7 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1328308 | 1328353 | 46 | 5 [3] | [2] 9 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1338218 | 1338228 | 11 | 4 [2] | [1] 4 | acnA | aconitate hydratase 1 |
| * | * | ÷ | W3110S.gb | 1371194 | 1371225 | 32 | 5 [0] | [1] 5 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | W3110S.gb | 1421314 | 1421323 | 10 | 5 [2] | [0] 4 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1828076 | 1828107 | 32 | 6 [2] | [0] 6 | astE | succinylglutamate desuccinylase |
| * | * | ÷ | W3110S.gb | 2041775 | 2041807 | 33 | 4 [3] | [0] 4 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2569094 | 2569139 | 46 | 6 [0] | [3] 4 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2827382 | 2827418 | 37 | 4 [1] | [3] 5 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 2893900 | 2893941 | 42 | 8 [3] | [3] 4 | ygcQ | predicted flavoprotein |
| * | * | ÷ | W3110S.gb | 3799043 | 3799063 | 21 | 6 [2] | [2] 4 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 3859261 | 3859314 | 54 | 5 [2] | [3] 4 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4213628–4216711 | 4216711 | 1–3084 | 4 [1] | [2] 4 | rrlE–[rrfE] | rrlE,[rrfE] |
| * | * | ÷ | W3110S.gb | 4401122 | 4401178 | 57 | 8 [3] | [1] 4 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 19 (0.490) | 93 (3.080) +CGCGTACAACT |
18/80 | NT | 71.9% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 74 (1.910) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 67 (1.730) | 33 (1.190) +AGGGTCCCTAAGTC |
13/74 | NT | 54.0% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 11 (0.280) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 205097 = | 34 (0.880) | 29 (1.010) +TTATAACATTTTA |
8/76 | NT | 49.5% | intergenic (+8/‑29) | rnhB/dnaE | ribonuclease HII, degrades RNA of DNA‑RNA hybrids/DNA polymerase III alpha subunit |
| ? | W3110S.gb | 4139149 = | 46 (1.190) | coding (2/1023 nt) | frlB | fructoselysine‑6‑P‑deglycase | |||||
| * | ? | W3110S.gb | = 236798 | 23 (0.600) | 47 (2.640) +27 bp |
23/48 | NT | 76.4% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 40 (1.030) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 40 (1.030) | 9/102 | 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 = | 28 (0.720) | 52 (1.400) +TC |
17/98 | NT | 79.5% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 46 (1.190) | 20/102 | 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) | 65 (1.680) | 18/102 | 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 = | 45 (1.160) | 112 (3.150) | 27/94 | NT | 70.4% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 53 (1.490) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 71 (1.840) | 190 (4.920) | 38/102 | NT | 73.5% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 66 (1.710) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 21 (0.540) | 8 (0.300) | 6/70 | NT | 33.8% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 17 (0.650) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 3 (0.080) | 15 (0.410) | 8/96 | NT | 84.2% | 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 | 0 (0.000) | 58 (1.560) | 19/98 | NT | 100% | 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 | 2172308 = | NA (NA) | 41 (1.080) | 17/100 | NT | 100% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 61 (1.610) | 17/100 | 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) | 34 (0.880) | 14/102 | 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) | 53 (1.370) | 22/102 | NT | 88.3% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 7 (0.180) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 2564137 = | 4 (0.100) | 6 (0.180) +ATGCGGT |
3/88 | NT | 31.0% | coding (1404/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase |
| ? | W3110S.gb | = 3997968 | 27 (0.700) | coding (684/753 nt) | yhiQ | predicted SAM‑dependent methyltransferase | |||||
| * | ? | W3110S.gb | 3748799 = | 6 (0.160) | 63 (1.630) | 24/102 | NT | 91.3% | 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 = | 1 (0.030) | 16 (0.500) | 6/84 | NT | 78.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 8 (0.250) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 1 (0.030) | 6 (0.190) | 5/84 | NT | 57.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 8 (0.250) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||