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 | 8,246 | C→T | 24.4% | D3D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,252 | G→A | 29.9% | L5L (TTG→TTA) | talB → | transaldolase B |
| RA | 8,255 | C→T | 29.5% | T6T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,258 | C→T | 29.5% | S7S (TCC→TCT) | talB → | transaldolase B |
| RA | 8,261 | T→G | 29.8% | L8L (CTT→CTG) | talB → | transaldolase B |
| RA | 8,276 | C→T | 45.7% | T13T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,279 | A→C | 47.0% | V14V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,282 | G→C | 47.4% | V15V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,285 | C→T | 47.5% | A16A (GCC→GCT) | talB → | transaldolase B |
| RA | 8,291 | T→C | 47.0% | T18T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,294 | G→A | 47.8% | G19G (GGG→GGA) | talB → | transaldolase B |
| RA | 8,297 | C→T | 47.4% | D20D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,300 | C→T | 47.0% | I21I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,321 | A→G | 51.2% | Q28Q (CAA→CAG) | talB → | transaldolase B |
| RA | 8,324 | G→T | 51.3% | P29P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,336 | A→C | 53.8% | T33T (ACA→ACC) | talB → | transaldolase B |
| RA | 8,339 | C→T | 54.4% | T34T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,348 | T→C | 57.3% | S37S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,351 | C→G | 57.3% | L38L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,357 | T→C | 57.2% | L40L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,358 | A→G | 57.6% | N41D (AAC→GAC) ‡ | talB → | transaldolase B |
| RA | 8,359 | A→G | 57.7% | N41S (AAC→AGC) ‡ | talB → | transaldolase B |
| RA | 8,363 | A→G | 60.1% | A42A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,366 | G→T | 60.2% | A43A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,372 | T→C | 63.4% | I45I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,375 | G→T | 64.5% | P46P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,378 | A→G | 63.8% | E47E (GAA→GAG) | talB → | transaldolase B |
| RA | 8,388 | T→C | 62.1% | L51L (TTG→CTG) | talB → | transaldolase B |
| RA | 8,396 | T→C | 63.9% | D53D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,399 | T→C | 64.5% | D54D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,414 | G→T | 52.1% | A59A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,415 | A→C | 52.1% | K60Q (AAA→CAA) ‡ | talB → | transaldolase B |
| RA | 8,416 | A→G | 52.1% | K60R (AAA→AGA) ‡ | talB → | transaldolase B |
| RA | 8,417 | A→T | 52.1% | K60N (AAA→AAT) ‡ | talB → | transaldolase B |
| RA | 8,419 | A→G | 51.7% | Q61R (CAG→CGG) ‡ | talB → | transaldolase B |
| RA | 8,420 | G→C | 51.7% | Q61H (CAG→CAC) ‡ | talB → | transaldolase B |
| RA | 8,428 | A→G | 57.1% | N64S (AAC→AGC) | talB → | transaldolase B |
| RA | 8,448 | G→C | 56.6% | V71L (GTG→CTG) ‡ | talB → | transaldolase B |
| RA | 8,450 | G→C | 56.2% | V71V (GTG→GTC) ‡ | talB → | transaldolase B |
| RA | 8,453 | C→T | 56.7% | D72D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,456 | G→T | 57.4% | A73A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,457 | A→T | 57.2% | T74S (ACC→TCC) | talB → | transaldolase B |
| RA | 8,462 | C→T | 57.0% | D75D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,465 | A→G | 58.6% | K76K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,471 | A→G | 60.7% | A78A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,474 | A→G | 59.6% | V79V (GTA→GTG) | talB → | transaldolase B |
| RA | 8,477 | T→C | 60.3% | N80N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,480 | T→C | 60.6% | I81I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,486 | G→C | 63.9% | L83L (CTG→CTC) | talB → | transaldolase B |
| RA | 8,492 | C→T | 61.4% | I85I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,502 | G→A | 63.8% | V89I (GTT→ATT) ‡ | talB → | transaldolase B |
| RA | 8,504 | T→C | 63.8% | V89V (GTT→GTC) ‡ | talB → | transaldolase B |
| RA | 8,519 | A→C | 64.1% | S94S (TCA→TCC) | talB → | transaldolase B |
| RA | 8,522 | T→C | 63.9% | T95T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,528 | T→G | 65.0% | V97V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,531 | T→C | 64.1% | D98D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,534 | G→A | 64.1% | A99A (GCG→GCA) | talB → | transaldolase B |
| RA | 8,540 | T→C | 66.2% | L101L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,561 | A→T | 75.7% | S108S (TCA→TCT) | talB → | transaldolase B |
| RA | 8,564 | T→C | 75.0% | I109I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,573 | A→C | 76.6% | A112A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,576 | A→G | 76.3% | K113K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,580 | C→A | 75.9% | L115M (CTG→ATG) ‡ | talB → | transaldolase B |
| RA | 8,582 | G→C | 75.7% | L115L (CTG→CTC) ‡ | talB → | transaldolase B |
| RA | 8,588 | A→G | 77.6% | K117K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,591 | C→G | 78.0% | L118L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,600 | T→C | 78.8% | D121D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,603 | T→G | 78.6% | A122A (GCT→GCG) | talB → | transaldolase B |
| RA | 8,606 | T→C | 79.2% | G123G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,609 | T→C | 79.1% | I124I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,621 | T→C | 81.6% | R128R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,639 | T→C | 83.7% | A134A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,642 | T→C | 83.3% | S135S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,654 | T→C | 86.4% | G139G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,657 | C→T | 86.1% | I140I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,660 | T→C | 85.1% | R141R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,663 | T→C | 85.1% | A142A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,666 | A→T | 84.9% | A143A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,690 | C→T | 86.3% | I151I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,705 | C→G | 86.1% | T156T (ACC→ACG) | talB → | transaldolase B |
| RA | 8,732 | T→C | 87.0% | R165R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,738 | T→C | 86.1% | C167C (TGT→TGC) | talB → | transaldolase B |
| RA | 8,741 | G→C | 87.2% | A168A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,753 | G→C | 88.6% | V172V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,762 | C→T | 88.3% | I175I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,771 | T→C | 87.5% | F178F (TTT→TTC) | talB → | transaldolase B |
| RA | 8,783 | T→C | 87.3% | I182I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,786 | T→C | 86.9% | L183L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,801 | G→C | 87.0% | A188A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,804 | T→C | 87.0% | N189N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,810 | T→C | 87.6% | D191D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,825 | T→A | 87.2% | A196A (GCT→GCA) | talB → | transaldolase B |
| RA | 8,852 | T→C | 85.7% | S205S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,855 | A→C | 84.7% | V206V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,856 | T→A | 84.9% | S207T (TCT→ACT) ‡ | talB → | transaldolase B |
| RA | 8,857 | C→G | 84.4% | S207C (TCT→TGT) ‡ | talB → | transaldolase B |
| RA | 8,858 | T→C | 84.4% | S207S (TCT→TCC) ‡ | talB → | transaldolase B |
| RA | 8,868 | C→G | 84.7% | Q211E (CAG→GAG) | talB → | transaldolase B |
| RA | 8,873 | C→T | 84.5% | Y212Y (TAC→TAT) | talB → | transaldolase B |
| RA | 8,879 | A→G | 84.2% | K214K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,880 | G→C | 83.4% | E215Q (GAG→CAG) | talB → | transaldolase B |
| RA | 8,888 | T→C | 82.9% | G217G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,900 | G→C | 82.7% | V221V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,903 | T→G | 82.1% | V222V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,925 | A→G | 82.3% | I230V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 8,927 | C→T | 82.3% | I230I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 8,948 | A→T | 78.5% | A237A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,954 | C→T | 79.4% | C239C (TGC→TGT) | talB → | transaldolase B |
| RA | 8,960 | T→C | 78.9% | R241R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,972 | A→C | 76.1% | A245A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,978 | A→G | 73.7% | A247A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,994 | G→T | 76.0% | A253S (GCG→TCG) ‡ | talB → | transaldolase B |
| RA | 8,996 | G→C | 76.3% | A253A (GCG→GCC) ‡ | talB → | transaldolase B |
| RA | 8,999 | G→A | 76.5% | E254E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,008 | G→C | 75.3% | G257G (GGG→GGC) | talB → | transaldolase B |
| RA | 9,011 | T→C | 75.7% | A258A (GCT→GCC) | talB → | transaldolase B |
| RA | 9,012 | A→G | 75.7% | I259V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 9,014 | C→T | 75.7% | I259I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 9,017 | A→G | 75.7% | E260E (GAA→GAG) | talB → | transaldolase B |
| RA | 9,023 | A→G | 74.9% | K262K (AAA→AAG) | talB → | transaldolase B |
| RA | 9,027 | T→G | 73.4% | S264A (TCT→GCT) ‡ | talB → | transaldolase B |
| RA | 9,028 | C→T | 72.7% | S264F (TCT→TTT) ‡ | talB → | transaldolase B |
| RA | 9,029 | T→A | 72.8% | S264S (TCT→TCA) ‡ | talB → | transaldolase B |
| RA | 9,032 | C→T | 73.7% | Y265Y (TAC→TAT) | talB → | transaldolase B |
| RA | 9,038 | C→T | 77.2% | G267G (GGC→GGT) | talB → | transaldolase B |
| RA | 9,058 | C→A | 76.8% | A274E (GCG→GAG) | talB → | transaldolase B |
| RA | 9,065 | C→T | 75.3% | I276I (ATC→ATT) | talB → | transaldolase B |
| RA | 9,068 | T→C | 74.7% | T277T (ACT→ACC) | talB → | transaldolase B |
| RA | 9,071 | G→A | 74.2% | E278E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,074 | C→T | 74.4% | S279S (TCC→TCT) | talB → | transaldolase B |
| RA | 9,092 | C→T | 73.5% | H285H (CAC→CAT) | talB → | transaldolase B |
| RA | 9,104 | A→G | 72.6% | P289P (CCA→CCG) | talB → | transaldolase B |
| RA | 9,110 | A→G | 70.4% | A291A (GCA→GCG) | talB → | transaldolase B |
| RA | 9,116 | T→C | 69.3% | D293D (GAT→GAC) | talB → | transaldolase B |
| RA | 9,146 | T→G | 56.9% | A303A (GCT→GCG) | talB → | transaldolase B |
| RA | 9,149 | T→C | 53.2% | I304I (ATT→ATC) | talB → | transaldolase B |
| RA | 9,178 | G→A | 43.5% | G314D (GGC→GAC) | talB → | transaldolase B |
| RA | 9,182 | T→A | 38.8% | D315E (GAT→GAA) | talB → | transaldolase B |
| RA | 360,147 | G→C | 27.0% | intergenic (‑81/+514) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,181 | G→C | 11.9% | intergenic (‑115/+480) | 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 |
| JC | 750,921 | +GCTATCT | 10.2% | coding (289/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| JC | 753,549 | Δ38 bp | 15.7% | coding (405‑442/717 nt) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 1,005,859 | G→A | 15.6% | G147E (GGG→GAG) | uup → | putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 1,191,676 | C→T | 41.0% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 35.6% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 29.3% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 29.2% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,733 | C→T | 24.3% | N385N (AAC→AAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,736 | G→C | 24.4% | A386A (GCG→GCC) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,739 | A→G | 23.7% | K387K (AAA→AAG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,484,009 | T→C | 37.8% | pseudogene (213/252 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,072 | G→A | 44.6% | 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 | 93.0% | intergenic (‑47/‑142) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,909,758 | C→A | 81.4% | E12* (GAA→TAA) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 1,930,220 | C→G | 14.8% | A118P (GCC→CCC) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| RA | 1,977,727 | A→C | 100% | I275R (ATA→AGA) | araG ← | fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components |
| MC JC | 2,093,044 | Δ2,186 bp | 100% | IS5‑mediated | [ugd]–wbbL | [ugd], gnd, wbbL |
| RA | 2,145,108 | G→A | 22.4% | R148K (AGA→AAA) | yegJ → | uncharacterized protein |
| RA | 2,145,170 | G→T | 36.1% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| JC JC | 2,770,391 | IS2 (+) +5 bp | 64.9% | coding (156‑160/201 nt) | ypjJ → | uncharacterized protein |
| RA | 2,960,118:1 | +C | 60.8% | coding (1676/2247 nt) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 2,978,089 | A→C | 25.5% | M288R (ATG→AGG) | yqeF ← | short chain acyltransferase |
| JC JC | 3,034,316 | IS2 (+) +5 bp | 68.2% | coding (110‑114/267 nt) | sdhE ← | flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair |
| RA | 3,074,446 | A→G | 6.2% | D183D (GAT→GAC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,454 | A→C | 10.7% | F181V (TTC→GTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,455 | T→G | 10.6% | A180A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,467 | A→G | 15.4% | G176G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,473 | C→T | 15.4% | K174K (AAG→AAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,478 | G→T | 15.3% | L173M (CTG→ATG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,481 | T→A | 15.1% | T172S (ACG→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,482 | A→G | 15.3% | G171G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,485 | C→T | 15.7% | A170A (GCG→GCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,490 | G→A | 15.8% | L169L (CTG→TTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,491 | A→T | 15.8% | S168S (TCT→TCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,498 | A→G | 15.9% | 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 | 17.8% | S163S (TCC→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,521 | C→T | 23.1% | M158I (ATG→ATA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,523 | T→A | 23.4% | M158L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,538 | T→G | 28.0% | M153L (ATG→CTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,563 | A→G | 27.4% | I144I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,566 | G→T | 27.3% | D143E (GAC→GAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,575 | C→G | 27.2% | P140P (CCG→CCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,578 | A→G | 26.7% | R139R (CGT→CGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,584 | A→G | 23.4% | F137F (TTT→TTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,587 | C→T | 23.0% | Q136Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,590 | C→G | 22.1% | A135A (GCG→GCC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,591 | G→C | 21.6% | A135G (GCG→GGG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,601 | T→C | 15.6% | T132A (ACG→GCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,602 | T→G | 15.4% | K131N (AAA→AAC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,603 | T→C | 15.6% | K131R (AAA→AGA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,604 | T→G | 15.4% | K131Q (AAA→CAA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,608 | T→G | 14.6% | A129A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,611 | A→T | 15.1% | I128I (ATT→ATA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,617 | C→G | 14.5% | M126I (ATG→ATC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,619 | T→A | 15.1% | M126L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,623 | G→C | 15.5% | V124V (GTC→GTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,626 | T→G | 13.0% | A123A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,629 | G→A | 15.8% | N122N (AAC→AAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,634 | C→T | 14.2% | A121T (GCC→ACC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,635 | A→G | 15.2% | I120I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,638 | A→G | 15.6% | G119G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,641 | C→T | 15.1% | Q118Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,647 | C→T | 13.3% | L116L (CTG→CTA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,649 | G→A | 13.3% | L116L (CTG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,653 | A→T | 11.7% | G114G (GGT→GGA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,659 | G→C | 8.5% | T112T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,662 | G→C | 8.4% | T111T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,433,446 | C→A | 100% | G315C (GGC→TGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,729,296 | A→C | 100% | K320Q (AAG→CAG) | xylR → | xylose divergent operon transcriptional activator |
| 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] | |
| JC | 4,224,391 | Δ12 bp | 78.6% | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1308898 | 1308955 | 58 | 28 [27] | [0] 57 | [ompW] | [ompW] |
| * | * | ÷ | CP009273 | 1857028 | 1858030 | 1003 | 65 [0] | [0] 46 | [gapA] | [gapA] |
| * | * | ÷ | CP009273 | 3099986 | 3100011 | 26 | 29 [26] | [25] 30 | nupG | nucleoside transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 320127 = | 22 (0.360) | 36 (0.580) | 35/276 | NT | 62.1% | 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 | 22 (0.360) | 34 (0.550) | 33/276 | NT | 60.7% | 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 = | 46 (0.740) | 57 (0.920) | 50/276 | NT | 55.3% | 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 | 360180 = | 45 (0.730) | 31 (0.910) +62 bp |
27/152 | NT | 71.4% | 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 | 454244 = | 4 (0.060) | 56 (0.930) | 52/268 | NT | 93.5% | 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 | 1 (0.020) | 48 (0.800) | 43/268 | NT | 98.0% | 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 | = 1092330 | 49 (0.790) | 7 (0.110) | 7/274 | NT | 12.6% | 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 | 1342452 = | 43 (0.700) | 5 (0.090) | 5/262 | NT | 10.4% | coding (718/1935 nt) | rnb | ribonuclease II |
| ? | CP009273 | = 1663663 | 45 (0.770) | coding (187/894 nt) | ynfL | LysR family putative transcriptional regulator | |||||
| * | ? | CP009273 | = 1406181 | 47 (0.760) | 4 (0.080) | 4/224 | NT | 8.6% | coding (25/936 nt) | ttcA | tRNA 2‑thiocytidine biosynthesis protein |
| ? | CP009273 | 1429242 = | 47 (0.940) | pseudogene (24/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1483968 = | NA (NA) | 46 (0.740) | 43/276 | 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 | 74 (1.200) | 38 (1.000) +53 bp |
33/170 | NT | 62.5% | 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 = | 54 (0.870) | 58 (0.950) | 53/274 | NT | 48.8% | coding (120/432 nt) | osmC | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| ? | CP009273 | = 1558191 | 68 (1.110) | coding (1800/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||
| * | ? | CP009273 | 3052022 = | 12 (0.190) | 1151 (18.890) +AG |
193/272 | NT | 99.0% | 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 = | 64 (1.040) | 314 (5.080) | 180/276 | NT | 83.1% | 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) | 60 (0.970) | 54/276 | 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) | 54 (0.870) | 50/276 | 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 = | 51 (0.830) | 6 (0.100) | 6/258 | NT | 9.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 71 (1.230) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||