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 | 8,261 | T→G | 5.7% | L8L (CTT→CTG) | talB → | transaldolase B |
| RA | 8,276 | C→T | 12.6% | T13T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,279 | A→C | 12.0% | V14V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,282 | G→C | 12.3% | V15V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,285 | C→T | 12.5% | A16A (GCC→GCT) | talB → | transaldolase B |
| RA | 8,291 | T→C | 11.7% | T18T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,294 | G→A | 13.0% | G19G (GGG→GGA) | talB → | transaldolase B |
| RA | 8,297 | C→T | 11.9% | D20D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,300 | C→T | 12.0% | I21I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,321 | A→G | 15.0% | Q28Q (CAA→CAG) | talB → | transaldolase B |
| RA | 8,324 | G→T | 15.1% | P29P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,336 | A→C | 21.3% | T33T (ACA→ACC) | talB → | transaldolase B |
| RA | 8,339 | C→T | 22.6% | T34T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,348 | T→C | 26.0% | S37S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,351 | C→G | 26.0% | L38L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,357 | T→C | 26.0% | L40L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,358 | A→G | 26.0% | N41D (AAC→GAC) ‡ | talB → | transaldolase B |
| RA | 8,359 | A→G | 26.1% | N41S (AAC→AGC) ‡ | talB → | transaldolase B |
| RA | 8,363 | A→G | 26.6% | A42A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,366 | G→T | 26.6% | A43A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,372 | T→C | 30.2% | I45I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,375 | G→T | 29.7% | P46P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,378 | A→G | 30.5% | E47E (GAA→GAG) | talB → | transaldolase B |
| RA | 8,388 | T→C | 33.4% | L51L (TTG→CTG) | talB → | transaldolase B |
| RA | 8,396 | T→C | 34.2% | D53D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,399 | T→C | 35.9% | D54D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,414 | G→T | 30.8% | A59A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,415 | A→C | 31.4% | K60Q (AAA→CAA) ‡ | talB → | transaldolase B |
| RA | 8,416 | A→G | 32.2% | K60R (AAA→AGA) ‡ | talB → | transaldolase B |
| RA | 8,417 | A→T | 31.7% | K60N (AAA→AAT) ‡ | talB → | transaldolase B |
| RA | 8,419 | A→G | 32.2% | Q61R (CAG→CGG) ‡ | talB → | transaldolase B |
| RA | 8,420 | G→C | 32.2% | Q61H (CAG→CAC) ‡ | talB → | transaldolase B |
| RA | 8,428 | A→G | 35.8% | N64S (AAC→AGC) | talB → | transaldolase B |
| RA | 8,448 | G→C | 41.4% | V71L (GTG→CTG) ‡ | talB → | transaldolase B |
| RA | 8,450 | G→C | 41.0% | V71V (GTG→GTC) ‡ | talB → | transaldolase B |
| RA | 8,453 | C→T | 41.3% | D72D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,456 | G→T | 43.5% | A73A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,457 | A→T | 43.0% | T74S (ACC→TCC) | talB → | transaldolase B |
| RA | 8,462 | C→T | 43.0% | D75D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,465 | A→G | 43.6% | K76K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,471 | A→G | 44.8% | A78A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,474 | A→G | 44.0% | V79V (GTA→GTG) | talB → | transaldolase B |
| RA | 8,477 | T→C | 42.7% | N80N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,480 | T→C | 41.8% | I81I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,486 | G→C | 43.2% | L83L (CTG→CTC) | talB → | transaldolase B |
| RA | 8,492 | C→T | 44.3% | I85I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,502 | G→A | 48.2% | V89I (GTT→ATT) ‡ | talB → | transaldolase B |
| RA | 8,504 | T→C | 47.8% | V89V (GTT→GTC) ‡ | talB → | transaldolase B |
| RA | 8,519 | A→C | 47.2% | S94S (TCA→TCC) | talB → | transaldolase B |
| RA | 8,522 | T→C | 47.2% | T95T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,528 | T→G | 51.7% | V97V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,531 | T→C | 50.0% | D98D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,534 | G→A | 49.7% | A99A (GCG→GCA) | talB → | transaldolase B |
| RA | 8,540 | T→C | 51.0% | L101L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,561 | A→T | 60.2% | S108S (TCA→TCT) | talB → | transaldolase B |
| RA | 8,564 | T→C | 60.2% | I109I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,573 | A→C | 63.0% | A112A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,576 | A→G | 62.4% | K113K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,580 | C→A | 62.3% | L115M (CTG→ATG) ‡ | talB → | transaldolase B |
| RA | 8,582 | G→C | 63.0% | L115L (CTG→CTC) ‡ | talB → | transaldolase B |
| RA | 8,588 | A→G | 65.2% | K117K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,591 | C→G | 63.8% | L118L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,600 | T→C | 67.2% | D121D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,603 | T→G | 66.9% | A122A (GCT→GCG) | talB → | transaldolase B |
| RA | 8,606 | T→C | 66.4% | G123G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,609 | T→C | 66.5% | I124I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,621 | T→C | 67.6% | R128R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,639 | T→C | 68.7% | A134A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,642 | T→C | 68.6% | S135S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,654 | T→C | 70.9% | G139G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,657 | C→T | 71.1% | I140I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,660 | T→C | 71.9% | R141R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,663 | T→C | 71.5% | A142A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,666 | A→T | 70.8% | A143A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,690 | C→T | 73.3% | I151I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,705 | C→G | 72.6% | T156T (ACC→ACG) | talB → | transaldolase B |
| RA | 8,732 | T→C | 72.6% | R165R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,738 | T→C | 72.7% | C167C (TGT→TGC) | talB → | transaldolase B |
| RA | 8,741 | G→C | 72.9% | A168A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,753 | G→C | 75.3% | V172V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,762 | C→T | 76.2% | I175I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,771 | T→C | 77.0% | F178F (TTT→TTC) | talB → | transaldolase B |
| RA | 8,783 | T→C | 79.0% | I182I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,786 | T→C | 78.4% | L183L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,801 | G→C | 79.4% | A188A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,804 | T→C | 79.2% | N189N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,810 | T→C | 80.0% | D191D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,825 | T→A | 79.6% | A196A (GCT→GCA) | talB → | transaldolase B |
| RA | 8,852 | T→C | 78.5% | S205S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,855 | A→C | 77.7% | V206V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,856 | T→A | 77.7% | S207T (TCT→ACT) ‡ | talB → | transaldolase B |
| RA | 8,857 | C→G | 76.7% | S207C (TCT→TGT) ‡ | talB → | transaldolase B |
| RA | 8,858 | T→C | 76.8% | S207S (TCT→TCC) ‡ | talB → | transaldolase B |
| RA | 8,868 | C→G | 78.2% | Q211E (CAG→GAG) | talB → | transaldolase B |
| RA | 8,873 | C→T | 78.4% | Y212Y (TAC→TAT) | talB → | transaldolase B |
| RA | 8,879 | A→G | 76.6% | K214K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,880 | G→C | 76.6% | E215Q (GAG→CAG) | talB → | transaldolase B |
| RA | 8,888 | T→C | 75.3% | G217G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,900 | G→C | 72.5% | V221V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,903 | T→G | 72.6% | V222V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,925 | A→G | 70.0% | I230V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 8,927 | C→T | 70.0% | I230I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 8,948 | A→T | 66.8% | A237A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,954 | C→T | 67.8% | C239C (TGC→TGT) | talB → | transaldolase B |
| RA | 8,960 | T→C | 67.0% | R241R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,972 | A→C | 64.9% | A245A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,978 | A→G | 64.0% | A247A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,994 | G→T | 64.4% | A253S (GCG→TCG) ‡ | talB → | transaldolase B |
| RA | 8,996 | G→C | 63.9% | A253A (GCG→GCC) ‡ | talB → | transaldolase B |
| RA | 8,999 | G→A | 64.0% | E254E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,008 | G→C | 64.1% | G257G (GGG→GGC) | talB → | transaldolase B |
| RA | 9,011 | T→C | 63.8% | A258A (GCT→GCC) | talB → | transaldolase B |
| RA | 9,012 | A→G | 63.9% | I259V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 9,014 | C→T | 63.9% | I259I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 9,017 | A→G | 62.3% | E260E (GAA→GAG) | talB → | transaldolase B |
| RA | 9,023 | A→G | 62.6% | K262K (AAA→AAG) | talB → | transaldolase B |
| RA | 9,027 | T→G | 58.6% | S264A (TCT→GCT) ‡ | talB → | transaldolase B |
| RA | 9,028 | C→T | 57.8% | S264F (TCT→TTT) ‡ | talB → | transaldolase B |
| RA | 9,029 | T→A | 58.6% | S264S (TCT→TCA) ‡ | talB → | transaldolase B |
| RA | 9,032 | C→T | 60.3% | Y265Y (TAC→TAT) | talB → | transaldolase B |
| RA | 9,038 | C→T | 64.3% | G267G (GGC→GGT) | talB → | transaldolase B |
| RA | 9,058 | C→A | 65.1% | A274E (GCG→GAG) | talB → | transaldolase B |
| RA | 9,065 | C→T | 62.1% | I276I (ATC→ATT) | talB → | transaldolase B |
| RA | 9,068 | T→C | 62.6% | T277T (ACT→ACC) | talB → | transaldolase B |
| RA | 9,071 | G→A | 62.6% | E278E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,074 | C→T | 61.8% | S279S (TCC→TCT) | talB → | transaldolase B |
| RA | 9,092 | C→T | 57.1% | H285H (CAC→CAT) | talB → | transaldolase B |
| RA | 9,104 | A→G | 56.2% | P289P (CCA→CCG) | talB → | transaldolase B |
| RA | 9,110 | A→G | 55.1% | A291A (GCA→GCG) | talB → | transaldolase B |
| RA | 9,116 | T→C | 54.6% | D293D (GAT→GAC) | talB → | transaldolase B |
| RA | 9,146 | T→G | 46.4% | A303A (GCT→GCG) | talB → | transaldolase B |
| RA | 9,149 | T→C | 44.1% | I304I (ATT→ATC) | talB → | transaldolase B |
| RA | 9,178 | G→A | 32.2% | G314D (GGC→GAC) | talB → | transaldolase B |
| RA | 9,182 | T→A | 31.0% | D315E (GAT→GAA) | talB → | transaldolase B |
| RA | 360,147 | G→C | 24.6% | intergenic (‑81/+514) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| JC | 374,639 | +GCCC | 100% | coding (389/1110 nt) | frmA ← | alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase |
| RA | 374,648 | Δ1 bp | 25.5% | coding (380/1110 nt) | frmA ← | alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase |
| RA | 455,197 | C→T | 12.6% | S285L (TCG→TTG) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 684,503:1 | +A | 14.3% | intergenic (‑34/+296) | insH1 ← / ← lnt | IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase |
| JC | 750,921 | +GCTATCT | 12.0% | coding (289/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| JC JC | 982,570 | IS5 (–) +4 bp | 24.4% | intergenic (‑132/+468) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,191,676 | C→T | 32.4% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 30.3% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 27.3% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 25.0% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,733 | C→T | 19.4% | N385N (AAC→AAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,736 | G→C | 19.4% | A386A (GCG→GCC) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,739 | A→G | 19.3% | K387K (AAA→AAG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,748 | C→T | 19.2% | T390T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,230,349 | T→C | 39.7% | intergenic (‑176/‑45) | nhaB ← / → fadR | sodium:proton antiporter/fatty acid metabolism regulon transcriptional regulator |
| RA | 1,484,009 | T→C | 47.4% | pseudogene (213/252 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,072 | G→A | 50.0% | pseudogene (150/252 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,221:1 | +T | 100% | pseudogene (1/252 nt) pseudogene (750/750 nt) |
gapC ← gapC ← |
pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,236 | C→G | 100% | pseudogene (735/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,239 | T→C | 100% | pseudogene (732/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,245 | T→C | 100% | pseudogene (726/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,404 | C→T | 100% | pseudogene (567/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,856 | A→T | 100% | pseudogene (115/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,919 | C→G | 100% | pseudogene (52/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,485,017 | A→G | 80.0% | intergenic (‑47/‑142) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,551,071 | C→T | 13.0% | L64F (CTT→TTT) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| RA | 1,551,119 | A→C | 18.8% | T80P (ACC→CCC) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| RA | 1,555,008 | T→C | 8.2% | D60G (GAC→GGC) | ddpB ← | D‑ala‑D‑ala transporter subunit |
| RA | 1,837,194 | T→A | 22.9% | N189K (AAT→AAA) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,909,758 | C→A | 37.9% | E12* (GAA→TAA) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 1,977,727 | A→C | 100% | I275R (ATA→AGA) | araG ← | fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 2,033,608 | T→C | 16.1% | L217P (CTC→CCC) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| MC JC | 2,093,044 | Δ2,186 bp | 100% | IS5‑mediated | [ugd]–wbbL | [ugd], gnd, wbbL |
| RA | 2,145,170 | G→T | 26.4% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| JC JC | 2,770,391 | IS2 (+) +5 bp | 47.0% | coding (156‑160/201 nt) | ypjJ → | uncharacterized protein |
| RA | 2,960,118:1 | +C | 66.0% | coding (1676/2247 nt) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 2,978,089 | A→C | 24.4% | M288R (ATG→AGG) | yqeF ← | short chain acyltransferase |
| JC JC | 3,034,316 | IS2 (+) +5 bp | 41.1% | coding (110‑114/267 nt) | sdhE ← | flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair |
| RA | 3,074,446 | A→G | 6.7% | D183D (GAT→GAC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,454 | A→C | 11.4% | F181V (TTC→GTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,455 | T→G | 11.4% | A180A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,467 | A→G | 15.2% | G176G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,473 | C→T | 14.8% | K174K (AAG→AAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,478 | G→T | 14.5% | L173M (CTG→ATG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,481 | T→A | 14.4% | T172S (ACG→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,482 | A→G | 14.6% | G171G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,485 | C→T | 14.7% | A170A (GCG→GCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,490 | G→A | 15.0% | L169L (CTG→TTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,491 | A→T | 15.0% | S168S (TCT→TCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,498 | A→G | 15.6% | V166A (GTT→GCT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,503 | G→A | 17.4% | H164H (CAC→CAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,506 | G→C | 18.0% | S163S (TCC→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,521 | C→T | 24.6% | M158I (ATG→ATA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,523 | T→A | 24.6% | M158L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,538 | T→G | 28.9% | M153L (ATG→CTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,563 | A→G | 28.2% | I144I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,566 | G→T | 28.4% | D143E (GAC→GAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,575 | C→G | 27.8% | P140P (CCG→CCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,578 | A→G | 27.4% | R139R (CGT→CGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,584 | A→G | 24.2% | F137F (TTT→TTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,587 | C→T | 24.0% | Q136Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,590 | C→G | 22.5% | A135A (GCG→GCC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,591 | G→C | 21.5% | A135G (GCG→GGG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,601 | T→C | 17.5% | T132A (ACG→GCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,602 | T→G | 17.3% | K131N (AAA→AAC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,603 | T→C | 17.1% | K131R (AAA→AGA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,604 | T→G | 16.9% | K131Q (AAA→CAA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,608 | T→G | 15.4% | A129A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,611 | A→T | 16.6% | I128I (ATT→ATA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,617 | C→G | 17.1% | M126I (ATG→ATC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,619 | T→A | 17.0% | M126L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,623 | G→C | 16.9% | V124V (GTC→GTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,626 | T→G | 12.7% | A123A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,629 | G→A | 16.8% | N122N (AAC→AAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,634 | C→T | 14.5% | A121T (GCC→ACC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,635 | A→G | 15.7% | I120I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,638 | A→G | 15.7% | G119G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,641 | C→T | 14.9% | Q118Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,647 | C→T | 13.6% | L116L (CTG→CTA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,649 | G→A | 14.1% | L116L (CTG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,653 | A→T | 12.8% | G114G (GGT→GGA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,659 | G→C | 8.0% | T112T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,662 | G→C | 7.8% | T111T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,303,385 | G→T | 8.9% | N381K (AAC→AAA) | pnp ← | polynucleotide phosphorylase/polyadenylase |
| RA | 3,433,446 | C→A | 100% | G315C (GGC→TGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,553,857 | G→A | 8.6% | R37C (CGC→TGC) | glpR ← | GlpR DNA‑binding transcriptional repressor |
| RA | 3,729,296 | A→C | 100% | K320Q (AAG→CAG) | xylR → | xylose divergent operon transcriptional activator |
| JC JC | 4,053,617 | IS4 (+) +12 bp | 18.1% | intergenic (+27/‑179) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,076,988 | Δ1 bp | 100% | coding (2195/3051 nt) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,097,480 | Δ1 bp | 100% | coding (1/963 nt) | pfkA → | 6‑phosphofructokinase I |
| MC JC | 4,097,486 | Δ962 bp | 100% | [pfkA] | [pfkA] | |
| RA | 4,141,257 | T→G | 15.8% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| JC | 4,224,391 | Δ12 bp | 47.2% | coding (706‑717/1650 nt) | pgi → | glucosephosphate isomerase |
| MC JC | 4,303,167 | Δ450 bp | 100% | coding (1‑450/450 nt) | rpiB → | ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase |
| JC | 4,629,587 | +ATT | 5.7% | coding (537/717 nt) | arcA ← | response regulator in two‑component regulatory system with ArcB or CpxA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1308899 | 1308955 | 57 | 30 [27] | [0] 70 | [ompW] | [ompW] |
| * | * | ÷ | CP009273 | 1857028 | 1858030 | 1003 | 63 [0] | [0] 63 | [gapA] | [gapA] |
| * | * | ÷ | CP009273 | 3099976 | 3100015 | 40 | 34 [27] | [27] 30 | nupG | nucleoside transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 15387 = | NA (NA) | 7 (0.110) | 7/268 | NT | 28.0% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | CP009273 | = 454251 | 18 (0.290) | intergenic (+95/‑93) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La | |||||
| * | ? | CP009273 | 320127 = | 33 (0.510) | 30 (0.470) | 29/276 | NT | 47.6% | coding (659/696 nt) | ykgG | LutC family protein; putative electron transport chain YkgEFG component |
| ? | CP009273 | 376716 = | NA (NA) | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA | |||||
| * | ? | CP009273 | = 320131 | 33 (0.510) | 21 (0.330) | 18/276 | NT | 38.9% | coding (663/696 nt) | ykgG | LutC family protein; putative electron transport chain YkgEFG component |
| ? | CP009273 | = 378046 | NA (NA) | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase | |||||
| * | ? | CP009273 | 360104 = | 45 (0.700) | 62 (0.970) | 49/276 | NT | 57.9% | 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 | 360180 = | 30 (0.470) | 41 (1.160) +62 bp |
37/152 | NT | 83.2% | intergenic (‑114/+481) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | 1308956 = | 0 (0.000) | intergenic (+41/+19) | ompW/yciE | outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein | |||||
| * | ? | CP009273 | 454243 = | 18 (0.280) | 12 (0.190) | 12/270 | NT | 40.5% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | = 604803 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | CP009273 | 454244 = | 18 (0.280) | 51 (0.820) | 46/268 | NT | 74.5% | intergenic (+88/‑100) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | 603467 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | CP009273 | = 454255 | 18 (0.280) | 36 (0.580) | 34/268 | NT | 67.3% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | = 604803 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | CP009273 | = 604803 | NA (NA) | 7 (0.110) | 7/270 | NT | 12.1% | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex |
| ? | CP009273 | 1297568 = | 52 (0.810) | coding (413/921 nt) | oppB | oligopeptide transporter subunit | |||||
| * | ? | CP009273 | 1092325 = | 72 (1.120) | 4 (0.060) | 4/276 | NT | 5.3% | intergenic (+40/+696) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | CP009273 | = 1463497 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | CP009273 | = 1092330 | 70 (1.090) | 11 (0.170) | 11/274 | NT | 13.7% | intergenic (+45/+691) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | CP009273 | = 1645804 | NA (NA) | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1203246 = | 10 (0.160) | 11 (0.190) | 10/244 | NT | 52.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 11 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 10 (0.160) | 15 (0.260) | 13/244 | NT | 60.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 11 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1297580 | 54 (0.840) | 13 (0.210) | 13/268 | NT | 19.9% | coding (425/921 nt) | oppB | oligopeptide transporter subunit |
| ? | CP009273 | 2507756 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | CP009273 | 1342452 = | 57 (0.890) | 4 (0.070) | 4/262 | NT | 6.7% | coding (718/1935 nt) | rnb | ribonuclease II |
| ? | CP009273 | = 1663663 | 57 (0.930) | coding (187/894 nt) | ynfL | LysR family putative transcriptional regulator | |||||
| * | ? | CP009273 | = 1463497 | NA (NA) | 4 (0.060) | 4/272 | NT | 6.7% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | CP009273 | 1747090 = | 56 (0.880) | coding (998/2103 nt) | ydhV | putative oxidoreductase subunit | |||||
| * | ? | CP009273 | 1483968 = | NA (NA) | 55 (0.860) | 46/276 | NT | 100% | intergenic (+40/+2) | aldA/gapC | aldehyde dehydrogenase A, NAD‑linked/pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| ? | CP009273 | 1858031 = | 0 (0.000) | intergenic (+8/‑76) | gapA/yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein | |||||
| * | ? | CP009273 | = 1485085 | 57 (0.890) | 38 (0.960) +53 bp |
32/170 | NT | 68.4% | intergenic (‑115/‑74) | gapC/cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| ? | CP009273 | = 1857027 | 0 (0.000) | intergenic (‑341/‑1) | msrB/gapA | methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A | |||||
| * | ? | CP009273 | 1551001 = | 55 (0.860) | 186 (2.920) | 126/274 | NT | 76.8% | coding (120/432 nt) | osmC | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| ? | CP009273 | = 1558191 | 58 (0.910) | coding (1800/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||
| * | ? | CP009273 | 3052022 = | 6 (0.090) | 645 (10.190) +AG |
176/272 | NT | 99.1% | intergenic (‑253/+3) | serA/rpiA | D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive |
| ? | CP009273 | 4161679 = | NA (NA) | noncoding (115/120 nt) | rrfB | 5S ribosomal RNA of rrnB operon | |||||
| * | ? | CP009273 | 3060603 = | 48 (0.750) | 164 (2.550) | 125/276 | NT | 77.4% | intergenic (‑71/+96) | ygfI/yggE | putative DNA‑binding transcriptional regulator/oxidative stress defense protein |
| ? | CP009273 | = 3124699 | NA (NA) | intergenic (+146/+1) | insH1/yghQ | IS5 transposase and trans‑activator/putative inner membrane polysaccharide flippase | |||||
| * | ? | CP009273 | 3179455 = | NA (NA) | 92 (1.430) | 76/276 | NT | 100% | intergenic (+7/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | CP009273 | = 3426721 | 0 (0.000) | coding (199/1125 nt) | smf | DNA recombination‑mediator A family protein | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 65 (1.010) | 56/276 | NT | 100% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | 3426717 = | 0 (0.000) | coding (203/1125 nt) | smf | DNA recombination‑mediator A family protein | |||||
| * | ? | CP009273 | 4532499 = | 65 (1.010) | 3 (0.050) | 3/258 | NT | 5.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 50 (0.830) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 65 (1.010) | 3 (0.050) | 3/258 | NT | 5.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 50 (0.830) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||