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 |
| JC | 3,536 | (CGGCAGGCG)2→1 | 14.0% | coding (736‑744/933 nt) | thrB → | homoserine kinase |
| RA | 8,246 | C→T | 10.2% | D3D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,252 | G→A | 10.9% | L5L (TTG→TTA) | talB → | transaldolase B |
| RA | 8,255 | C→T | 10.5% | T6T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,258 | C→T | 11.1% | S7S (TCC→TCT) | talB → | transaldolase B |
| RA | 8,261 | T→G | 11.1% | L8L (CTT→CTG) | talB → | transaldolase B |
| RA | 8,276 | C→T | 15.2% | T13T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,279 | A→C | 15.9% | V14V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,282 | G→C | 16.4% | V15V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,285 | C→T | 18.3% | A16A (GCC→GCT) | talB → | transaldolase B |
| RA | 8,291 | T→C | 15.1% | T18T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,294 | G→A | 15.1% | G19G (GGG→GGA) | talB → | transaldolase B |
| RA | 8,297 | C→T | 15.3% | D20D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,300 | C→T | 15.7% | I21I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,321 | A→G | 20.2% | Q28Q (CAA→CAG) | talB → | transaldolase B |
| RA | 8,324 | G→T | 19.3% | P29P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,336 | A→C | 25.0% | T33T (ACA→ACC) | talB → | transaldolase B |
| RA | 8,339 | C→T | 26.2% | T34T (ACC→ACT) | talB → | transaldolase B |
| RA | 8,348 | T→C | 26.6% | S37S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,351 | C→G | 26.6% | L38L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,357 | T→C | 27.3% | L40L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,358 | A→G | 27.2% | N41D (AAC→GAC) ‡ | talB → | transaldolase B |
| RA | 8,359 | A→G | 27.6% | N41S (AAC→AGC) ‡ | talB → | transaldolase B |
| RA | 8,363 | A→G | 28.7% | A42A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,366 | G→T | 28.7% | A43A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,372 | T→C | 31.8% | I45I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,375 | G→T | 31.6% | P46P (CCG→CCT) | talB → | transaldolase B |
| RA | 8,378 | A→G | 31.7% | E47E (GAA→GAG) | talB → | transaldolase B |
| RA | 8,388 | T→C | 35.3% | L51L (TTG→CTG) | talB → | transaldolase B |
| RA | 8,396 | T→C | 36.6% | D53D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,399 | T→C | 37.5% | D54D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,414 | G→T | 32.7% | A59A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,415 | A→C | 33.0% | K60Q (AAA→CAA) ‡ | talB → | transaldolase B |
| RA | 8,416 | A→G | 33.0% | K60R (AAA→AGA) ‡ | talB → | transaldolase B |
| RA | 8,417 | A→T | 33.0% | K60N (AAA→AAT) ‡ | talB → | transaldolase B |
| RA | 8,419 | A→G | 33.1% | Q61R (CAG→CGG) ‡ | talB → | transaldolase B |
| RA | 8,420 | G→C | 33.6% | Q61H (CAG→CAC) ‡ | talB → | transaldolase B |
| RA | 8,428 | A→G | 38.4% | N64S (AAC→AGC) | talB → | transaldolase B |
| RA | 8,448 | G→C | 41.1% | V71L (GTG→CTG) ‡ | talB → | transaldolase B |
| RA | 8,450 | G→C | 40.5% | V71V (GTG→GTC) ‡ | talB → | transaldolase B |
| RA | 8,453 | C→T | 42.4% | D72D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,456 | G→T | 43.8% | A73A (GCG→GCT) | talB → | transaldolase B |
| RA | 8,457 | A→T | 43.1% | T74S (ACC→TCC) | talB → | transaldolase B |
| RA | 8,462 | C→T | 43.1% | D75D (GAC→GAT) | talB → | transaldolase B |
| RA | 8,465 | A→G | 43.2% | K76K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,471 | A→G | 44.9% | A78A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,474 | A→G | 42.7% | V79V (GTA→GTG) | talB → | transaldolase B |
| RA | 8,477 | T→C | 42.7% | N80N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,480 | T→C | 42.4% | I81I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,486 | G→C | 46.8% | L83L (CTG→CTC) | talB → | transaldolase B |
| RA | 8,492 | C→T | 50.0% | I85I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,502 | G→A | 53.8% | V89I (GTT→ATT) ‡ | talB → | transaldolase B |
| RA | 8,504 | T→C | 54.6% | V89V (GTT→GTC) ‡ | talB → | transaldolase B |
| RA | 8,519 | A→C | 53.4% | S94S (TCA→TCC) | talB → | transaldolase B |
| RA | 8,522 | T→C | 53.0% | T95T (ACT→ACC) | talB → | transaldolase B |
| RA | 8,528 | T→G | 55.4% | V97V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,531 | T→C | 53.0% | D98D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,534 | G→A | 52.4% | A99A (GCG→GCA) | talB → | transaldolase B |
| RA | 8,540 | T→C | 53.0% | L101L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,561 | A→T | 63.2% | S108S (TCA→TCT) | talB → | transaldolase B |
| RA | 8,564 | T→C | 62.1% | I109I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,573 | A→C | 62.3% | A112A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,576 | A→G | 60.8% | K113K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,580 | C→A | 60.3% | L115M (CTG→ATG) ‡ | talB → | transaldolase B |
| RA | 8,582 | G→C | 60.3% | L115L (CTG→CTC) ‡ | talB → | transaldolase B |
| RA | 8,588 | A→G | 64.1% | K117K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,591 | C→G | 64.6% | L118L (CTC→CTG) | talB → | transaldolase B |
| RA | 8,600 | T→C | 66.8% | D121D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,603 | T→G | 67.0% | A122A (GCT→GCG) | talB → | transaldolase B |
| RA | 8,606 | T→C | 67.4% | G123G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,609 | T→C | 68.4% | I124I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,621 | T→C | 70.6% | R128R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,639 | T→C | 70.3% | A134A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,642 | T→C | 69.7% | S135S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,654 | T→C | 70.8% | G139G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,657 | C→T | 70.2% | I140I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,660 | T→C | 70.2% | R141R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,663 | T→C | 70.2% | A142A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,666 | A→T | 69.0% | A143A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,690 | C→T | 73.2% | I151I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,705 | C→G | 74.3% | T156T (ACC→ACG) | talB → | transaldolase B |
| RA | 8,732 | T→C | 74.0% | R165R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,738 | T→C | 74.8% | C167C (TGT→TGC) | talB → | transaldolase B |
| RA | 8,741 | G→C | 73.6% | A168A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,753 | G→C | 75.2% | V172V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,762 | C→T | 74.3% | I175I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,771 | T→C | 75.2% | F178F (TTT→TTC) | talB → | transaldolase B |
| RA | 8,783 | T→C | 76.4% | I182I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,786 | T→C | 76.3% | L183L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,801 | G→C | 78.5% | A188A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,804 | T→C | 78.5% | N189N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,810 | T→C | 79.6% | D191D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,825 | T→A | 79.9% | A196A (GCT→GCA) | talB → | transaldolase B |
| RA | 8,852 | T→C | 78.1% | S205S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,855 | A→C | 77.1% | V206V (GTA→GTC) | talB → | transaldolase B |
| RA | 8,856 | T→A | 77.4% | S207T (TCT→ACT) ‡ | talB → | transaldolase B |
| RA | 8,857 | C→G | 77.4% | S207C (TCT→TGT) ‡ | talB → | transaldolase B |
| RA | 8,858 | T→C | 78.0% | S207S (TCT→TCC) ‡ | talB → | transaldolase B |
| RA | 8,868 | C→G | 78.6% | Q211E (CAG→GAG) | talB → | transaldolase B |
| RA | 8,873 | C→T | 78.2% | Y212Y (TAC→TAT) | talB → | transaldolase B |
| RA | 8,879 | A→G | 76.1% | K214K (AAA→AAG) | talB → | transaldolase B |
| RA | 8,880 | G→C | 75.4% | E215Q (GAG→CAG) | talB → | transaldolase B |
| RA | 8,888 | T→C | 75.6% | G217G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,900 | G→C | 73.7% | V221V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,903 | T→G | 73.8% | V222V (GTT→GTG) | talB → | transaldolase B |
| RA | 8,925 | A→G | 70.8% | I230V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 8,927 | C→T | 70.5% | I230I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 8,948 | A→T | 66.1% | A237A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,954 | C→T | 66.0% | C239C (TGC→TGT) | talB → | transaldolase B |
| RA | 8,960 | T→C | 62.9% | R241R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,972 | A→C | 56.8% | A245A (GCA→GCC) | talB → | transaldolase B |
| RA | 8,978 | A→G | 54.7% | A247A (GCA→GCG) | talB → | transaldolase B |
| RA | 8,994 | G→T | 55.7% | A253S (GCG→TCG) ‡ | talB → | transaldolase B |
| RA | 8,996 | G→C | 56.1% | A253A (GCG→GCC) ‡ | talB → | transaldolase B |
| RA | 8,999 | G→A | 56.1% | E254E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,008 | G→C | 57.0% | G257G (GGG→GGC) | talB → | transaldolase B |
| RA | 9,011 | T→C | 57.0% | A258A (GCT→GCC) | talB → | transaldolase B |
| RA | 9,012 | A→G | 57.1% | I259V (ATC→GTC) ‡ | talB → | transaldolase B |
| RA | 9,014 | C→T | 57.8% | I259I (ATC→ATT) ‡ | talB → | transaldolase B |
| RA | 9,017 | A→G | 57.4% | E260E (GAA→GAG) | talB → | transaldolase B |
| RA | 9,023 | A→G | 57.2% | K262K (AAA→AAG) | talB → | transaldolase B |
| RA | 9,027 | T→G | 53.4% | S264A (TCT→GCT) ‡ | talB → | transaldolase B |
| RA | 9,028 | C→T | 52.3% | S264F (TCT→TTT) ‡ | talB → | transaldolase B |
| RA | 9,029 | T→A | 52.7% | S264S (TCT→TCA) ‡ | talB → | transaldolase B |
| RA | 9,032 | C→T | 52.7% | Y265Y (TAC→TAT) | talB → | transaldolase B |
| RA | 9,038 | C→T | 55.5% | G267G (GGC→GGT) | talB → | transaldolase B |
| RA | 9,058 | C→A | 57.1% | A274E (GCG→GAG) | talB → | transaldolase B |
| RA | 9,065 | C→T | 54.4% | I276I (ATC→ATT) | talB → | transaldolase B |
| RA | 9,068 | T→C | 53.5% | T277T (ACT→ACC) | talB → | transaldolase B |
| RA | 9,071 | G→A | 55.2% | E278E (GAG→GAA) | talB → | transaldolase B |
| RA | 9,074 | C→T | 53.8% | S279S (TCC→TCT) | talB → | transaldolase B |
| RA | 9,092 | C→T | 52.8% | H285H (CAC→CAT) | talB → | transaldolase B |
| RA | 9,104 | A→G | 53.2% | P289P (CCA→CCG) | talB → | transaldolase B |
| RA | 9,110 | A→G | 51.8% | A291A (GCA→GCG) | talB → | transaldolase B |
| RA | 9,116 | T→C | 52.2% | D293D (GAT→GAC) | talB → | transaldolase B |
| RA | 9,146 | T→G | 41.9% | A303A (GCT→GCG) | talB → | transaldolase B |
| RA | 9,149 | T→C | 37.7% | I304I (ATT→ATC) | talB → | transaldolase B |
| RA | 9,178 | G→A | 29.0% | G314D (GGC→GAC) | talB → | transaldolase B |
| RA | 9,182 | T→A | 28.3% | D315E (GAT→GAA) | talB → | transaldolase B |
| JC | 154,980 | Δ18 bp | 13.7% | coding (617‑634/1398 nt) | pcnB ← | poly(A) polymerase |
| RA | 225,842 | T→C | 5.8% | T63T (ACT→ACC) | dkgB → | 2,5‑diketo‑D‑gluconate reductase B |
| RA | 360,147 | G→C | 23.9% | intergenic (‑81/+514) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,181 | G→C | 13.0% | 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 |
| RA | 374,648 | Δ1 bp | 54.4% | coding (380/1110 nt) | frmA ← | alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase |
| RA | 416,070 | Δ1 bp | 6.0% | coding (1024/1320 nt) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 684,503:1 | +A | 70.5% | intergenic (‑34/+296) | insH1 ← / ← lnt | IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase |
| JC JC | 982,570 | IS5 (–) +4 bp | 52.0% | intergenic (‑132/+468) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,005,859 | G→A | 20.4% | G147E (GGG→GAG) | uup → | putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 1,039,559 | G→A | 6.7% | S36S (AGC→AGT) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,191,676 | C→T | 8.9% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 9.2% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,230,349 | T→C | 46.5% | intergenic (‑176/‑45) | nhaB ← / → fadR | sodium:proton antiporter/fatty acid metabolism regulon transcriptional regulator |
| JC JC | 1,254,388 | IS5 (+) +4 bp | 27.1% | coding (142‑145/279 nt) | ychH → | DUF2583 family putative inner membrane protein |
| RA | 1,484,009 | T→C | 50.4% | pseudogene (213/252 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,072 | G→A | 49.7% | 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 | 68.5% | intergenic (‑47/‑142) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,566,793 | G→A | 8.5% | D889D (GAC→GAT) | pqqL ← | putative periplasmic M16 family zinc metalloendopeptidase |
| RA | 1,909,758 | C→A | 20.7% | E12* (GAA→TAA) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 1,930,220 | C→G | 24.2% | 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 |
| JC | 2,066,645 | Δ18 bp | 11.5% | coding (1626‑1643/3120 nt) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| MC JC | 2,093,044 | Δ2,186 bp | 100% | IS5‑mediated | [ugd]–wbbL | [ugd], gnd, wbbL |
| RA | 2,797,928 | C→T | 5.6% | intergenic (+108/‑246) | nrdF → / → proV | ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like protein/glycine betaine transporter subunit |
| RA | 2,960,118:1 | +C | 28.3% | coding (1676/2247 nt) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 3,074,446 | A→G | 5.8% | 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 | 16.4% | G176G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,473 | C→T | 14.7% | 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 | 14.6% | T172S (ACG→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,482 | A→G | 14.5% | G171G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,485 | C→T | 14.8% | A170A (GCG→GCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,490 | G→A | 14.6% | L169L (CTG→TTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,491 | A→T | 14.6% | S168S (TCT→TCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,498 | A→G | 14.5% | V166A (GTT→GCT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,503 | G→A | 17.7% | H164H (CAC→CAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,506 | G→C | 17.9% | S163S (TCC→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,521 | C→T | 20.2% | M158I (ATG→ATA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,523 | T→A | 20.2% | M158L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,538 | T→G | 24.8% | M153L (ATG→CTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,563 | A→G | 24.2% | I144I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,566 | G→T | 24.3% | D143E (GAC→GAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,575 | C→G | 24.0% | P140P (CCG→CCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,578 | A→G | 23.9% | R139R (CGT→CGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,584 | A→G | 20.6% | F137F (TTT→TTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,587 | C→T | 20.7% | Q136Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,590 | C→G | 18.5% | A135A (GCG→GCC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,591 | G→C | 18.1% | A135G (GCG→GGG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,601 | T→C | 12.9% | T132A (ACG→GCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,602 | T→G | 13.3% | K131N (AAA→AAC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,603 | T→C | 13.2% | K131R (AAA→AGA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,604 | T→G | 13.2% | K131Q (AAA→CAA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,608 | T→G | 12.9% | A129A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,611 | A→T | 13.0% | I128I (ATT→ATA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,617 | C→G | 13.2% | M126I (ATG→ATC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,619 | T→A | 13.2% | M126L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,623 | G→C | 13.4% | V124V (GTC→GTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,626 | T→G | 11.1% | A123A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,629 | G→A | 13.2% | N122N (AAC→AAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,634 | C→T | 12.2% | A121T (GCC→ACC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,635 | A→G | 12.5% | I120I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,638 | A→G | 12.5% | G119G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,641 | C→T | 12.4% | Q118Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,647 | C→T | 9.5% | L116L (CTG→CTA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,649 | G→A | 9.5% | L116L (CTG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,653 | A→T | 8.4% | G114G (GGT→GGA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,659 | G→C | 7.4% | T112T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,074,662 | G→C | 7.5% | T111T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,433,446 | C→A | 100% | G315C (GGC→TGC) | rpoA ← | RNA polymerase, alpha subunit |
| JC | 3,553,266 | Δ8 bp | 12.4% | coding (693‑700/759 nt) | glpR ← | GlpR DNA‑binding transcriptional repressor |
| RA | 3,602,774 | G→T | 6.0% | P66P (CCG→CCT) | yhhQ → | DUF165 family inner membrane protein |
| RA | 3,729,296 | A→C | 100% | K320Q (AAG→CAG) | xylR → | xylose divergent operon transcriptional activator |
| RA | 3,856,021 | T→G | 24.8% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| JC JC | 4,053,617 | IS4 (+) +12 bp | 30.6% | 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] | |
| JC | 4,224,391 | Δ12 bp | 12.0% | 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 |
| RA | 4,582,841 | G→T | 7.4% | M456I (ATG→ATT) | tsr → | methyl‑accepting chemotaxis protein I, serine sensor receptor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1308888 | 1308955 | 68 | 27 [26] | [0] 61 | [ompW] | [ompW] |
| * | * | ÷ | CP009273 | 1857028 | 1858030 | 1003 | 59 [0] | [0] 66 | [gapA] | [gapA] |
| * | * | ÷ | CP009273 | 3099986 | 3100018 | 33 | 27 [24] | [26] 27 | nupG | nucleoside transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 15387 = | NA (NA) | 5 (0.090) | 5/268 | NT | 13.9% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | CP009273 | = 454251 | 31 (0.560) | intergenic (+95/‑93) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La | |||||
| * | ? | CP009273 | = 287112 | NA (NA) | 4 (0.070) | 4/276 | NT | 8.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | CP009273 | 2382388 = | 45 (0.780) | coding (275/423 nt) | yfbO | uncharacterized protein | |||||
| * | ? | CP009273 | 360104 = | 52 (0.900) | 54 (0.940) | 49/276 | NT | 50.9% | 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 = | 58 (1.010) | 31 (0.980) +62 bp |
27/152 | NT | 66.1% | 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 = | 31 (0.540) | 7 (0.120) | 7/270 | NT | 18.8% | 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 = | 31 (0.540) | 22 (0.390) | 21/268 | NT | 42.2% | 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 | 31 (0.540) | 24 (0.430) | 23/268 | NT | 44.4% | 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) | 35 (0.620) | 31/270 | NT | 48.5% | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex |
| ? | CP009273 | 1297568 = | 38 (0.660) | coding (413/921 nt) | oppB | oligopeptide transporter subunit | |||||
| * | ? | CP009273 | 1203246 = | 25 (0.430) | 10 (0.200) | 9/244 | NT | 28.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 29 (0.570) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 27 (0.470) | 11 (0.220) | 11/244 | NT | 29.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 29 (0.570) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1297580 | 38 (0.660) | 22 (0.390) | 20/268 | NT | 37.4% | coding (425/921 nt) | oppB | oligopeptide transporter subunit |
| ? | CP009273 | 2507756 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | CP009273 | 1483968 = | NA (NA) | 65 (1.130) | 52/276 | 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 | 75 (1.300) | 35 (0.990) +53 bp |
28/170 | NT | 60.4% | 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 = | 49 (0.850) | 68 (1.190) | 59/274 | NT | 58.5% | coding (120/432 nt) | osmC | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| ? | CP009273 | = 1558191 | 48 (0.840) | coding (1800/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||
| * | ? | CP009273 | 3052022 = | 11 (0.190) | 949 (16.750) +AG |
193/272 | NT | 98.9% | 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 = | 49 (0.850) | 129 (2.240) | 97/276 | NT | 72.5% | 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) | 63 (1.100) | 52/276 | 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) | 66 (1.150) | 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 | |||||