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 | 15.7% | D3D (GAC→GAT) | talB → | transaldolase B |
RA | 8,252 | G→A | 23.0% | L5L (TTG→TTA) | talB → | transaldolase B |
RA | 8,255 | C→T | 23.5% | T6T (ACC→ACT) | talB → | transaldolase B |
RA | 8,258 | C→T | 22.8% | S7S (TCC→TCT) | talB → | transaldolase B |
RA | 8,261 | T→G | 23.0% | L8L (CTT→CTG) | talB → | transaldolase B |
RA | 8,276 | C→T | 32.1% | T13T (ACC→ACT) | talB → | transaldolase B |
RA | 8,279 | A→C | 30.5% | V14V (GTA→GTC) | talB → | transaldolase B |
RA | 8,282 | G→C | 30.2% | V15V (GTG→GTC) | talB → | transaldolase B |
RA | 8,285 | C→T | 30.5% | A16A (GCC→GCT) | talB → | transaldolase B |
RA | 8,291 | T→C | 30.5% | T18T (ACT→ACC) | talB → | transaldolase B |
RA | 8,294 | G→A | 31.2% | G19G (GGG→GGA) | talB → | transaldolase B |
RA | 8,297 | C→T | 30.5% | D20D (GAC→GAT) | talB → | transaldolase B |
RA | 8,300 | C→T | 30.5% | I21I (ATC→ATT) | talB → | transaldolase B |
RA | 8,321 | A→G | 36.0% | Q28Q (CAA→CAG) | talB → | transaldolase B |
RA | 8,324 | G→T | 35.7% | P29P (CCG→CCT) | talB → | transaldolase B |
RA | 8,336 | A→C | 39.1% | T33T (ACA→ACC) | talB → | transaldolase B |
RA | 8,339 | C→T | 39.0% | T34T (ACC→ACT) | talB → | transaldolase B |
RA | 8,348 | T→C | 42.5% | S37S (TCT→TCC) | talB → | transaldolase B |
RA | 8,351 | C→G | 42.5% | L38L (CTC→CTG) | talB → | transaldolase B |
RA | 8,357 | T→C | 41.8% | L40L (CTT→CTC) | talB → | transaldolase B |
RA | 8,358 | A→G | 41.8% | N41D (AAC→GAC) ‡ | talB → | transaldolase B |
RA | 8,359 | A→G | 41.8% | N41S (AAC→AGC) ‡ | talB → | transaldolase B |
RA | 8,363 | A→G | 42.2% | A42A (GCA→GCG) | talB → | transaldolase B |
RA | 8,366 | G→T | 42.1% | A43A (GCG→GCT) | talB → | transaldolase B |
RA | 8,372 | T→C | 44.2% | I45I (ATT→ATC) | talB → | transaldolase B |
RA | 8,375 | G→T | 44.9% | P46P (CCG→CCT) | talB → | transaldolase B |
RA | 8,378 | A→G | 44.6% | E47E (GAA→GAG) | talB → | transaldolase B |
RA | 8,388 | T→C | 37.5% | L51L (TTG→CTG) | talB → | transaldolase B |
RA | 8,396 | T→C | 37.6% | D53D (GAT→GAC) | talB → | transaldolase B |
RA | 8,399 | T→C | 39.2% | D54D (GAT→GAC) | talB → | transaldolase B |
RA | 8,414 | G→T | 31.5% | A59A (GCG→GCT) | talB → | transaldolase B |
RA | 8,415 | A→C | 31.5% | K60Q (AAA→CAA) ‡ | talB → | transaldolase B |
RA | 8,416 | A→G | 31.5% | K60R (AAA→AGA) ‡ | talB → | transaldolase B |
RA | 8,417 | A→T | 31.8% | K60N (AAA→AAT) ‡ | talB → | transaldolase B |
RA | 8,419 | A→G | 31.5% | Q61R (CAG→CGG) ‡ | talB → | transaldolase B |
RA | 8,420 | G→C | 31.6% | Q61H (CAG→CAC) ‡ | talB → | transaldolase B |
RA | 8,428 | A→G | 37.1% | N64S (AAC→AGC) | talB → | transaldolase B |
RA | 8,448 | G→C | 40.8% | V71L (GTG→CTG) ‡ | talB → | transaldolase B |
RA | 8,450 | G→C | 40.1% | V71V (GTG→GTC) ‡ | talB → | transaldolase B |
RA | 8,453 | C→T | 41.2% | D72D (GAC→GAT) | talB → | transaldolase B |
RA | 8,456 | G→T | 42.4% | A73A (GCG→GCT) | talB → | transaldolase B |
RA | 8,457 | A→T | 41.5% | T74S (ACC→TCC) | talB → | transaldolase B |
RA | 8,462 | C→T | 41.6% | D75D (GAC→GAT) | talB → | transaldolase B |
RA | 8,465 | A→G | 45.4% | K76K (AAA→AAG) | talB → | transaldolase B |
RA | 8,471 | A→G | 46.7% | A78A (GCA→GCG) | talB → | transaldolase B |
RA | 8,474 | A→G | 48.2% | V79V (GTA→GTG) | talB → | transaldolase B |
RA | 8,477 | T→C | 47.8% | N80N (AAT→AAC) | talB → | transaldolase B |
RA | 8,480 | T→C | 46.2% | I81I (ATT→ATC) | talB → | transaldolase B |
RA | 8,486 | G→C | 47.5% | L83L (CTG→CTC) | talB → | transaldolase B |
RA | 8,492 | C→T | 46.7% | I85I (ATC→ATT) | talB → | transaldolase B |
RA | 8,502 | G→A | 48.3% | V89I (GTT→ATT) ‡ | talB → | transaldolase B |
RA | 8,504 | T→C | 48.8% | V89V (GTT→GTC) ‡ | talB → | transaldolase B |
RA | 8,519 | A→C | 50.8% | S94S (TCA→TCC) | talB → | transaldolase B |
RA | 8,522 | T→C | 49.6% | T95T (ACT→ACC) | talB → | transaldolase B |
RA | 8,528 | T→G | 52.0% | V97V (GTT→GTG) | talB → | transaldolase B |
RA | 8,531 | T→C | 52.0% | D98D (GAT→GAC) | talB → | transaldolase B |
RA | 8,534 | G→A | 52.2% | A99A (GCG→GCA) | talB → | transaldolase B |
RA | 8,540 | T→C | 50.4% | L101L (CTT→CTC) | talB → | transaldolase B |
RA | 8,561 | A→T | 62.6% | S108S (TCA→TCT) | talB → | transaldolase B |
RA | 8,564 | T→C | 61.2% | I109I (ATT→ATC) | talB → | transaldolase B |
RA | 8,573 | A→C | 63.7% | A112A (GCA→GCC) | talB → | transaldolase B |
RA | 8,576 | A→G | 62.2% | K113K (AAA→AAG) | talB → | transaldolase B |
RA | 8,580 | C→A | 61.6% | L115M (CTG→ATG) ‡ | talB → | transaldolase B |
RA | 8,582 | G→C | 62.0% | L115L (CTG→CTC) ‡ | talB → | transaldolase B |
RA | 8,588 | A→G | 63.5% | K117K (AAA→AAG) | talB → | transaldolase B |
RA | 8,591 | C→G | 63.5% | L118L (CTC→CTG) | talB → | transaldolase B |
RA | 8,600 | T→C | 66.1% | D121D (GAT→GAC) | talB → | transaldolase B |
RA | 8,603 | T→G | 65.6% | A122A (GCT→GCG) | talB → | transaldolase B |
RA | 8,606 | T→C | 64.3% | G123G (GGT→GGC) | talB → | transaldolase B |
RA | 8,609 | T→C | 62.4% | I124I (ATT→ATC) | talB → | transaldolase B |
RA | 8,621 | T→C | 67.5% | R128R (CGT→CGC) | talB → | transaldolase B |
RA | 8,639 | T→C | 69.7% | A134A (GCT→GCC) | talB → | transaldolase B |
RA | 8,642 | T→C | 69.3% | S135S (TCT→TCC) | talB → | transaldolase B |
RA | 8,654 | T→C | 71.1% | G139G (GGT→GGC) | talB → | transaldolase B |
RA | 8,657 | C→T | 71.3% | I140I (ATC→ATT) | talB → | transaldolase B |
RA | 8,660 | T→C | 69.8% | R141R (CGT→CGC) | talB → | transaldolase B |
RA | 8,663 | T→C | 69.8% | A142A (GCT→GCC) | talB → | transaldolase B |
RA | 8,666 | A→T | 68.8% | A143A (GCA→GCT) | talB → | transaldolase B |
RA | 8,690 | C→T | 73.3% | I151I (ATC→ATT) | talB → | transaldolase B |
RA | 8,705 | C→G | 71.4% | T156T (ACC→ACG) | talB → | transaldolase B |
RA | 8,732 | T→C | 70.6% | R165R (CGT→CGC) | talB → | transaldolase B |
RA | 8,738 | T→C | 69.3% | C167C (TGT→TGC) | talB → | transaldolase B |
RA | 8,741 | G→C | 70.4% | A168A (GCG→GCC) | talB → | transaldolase B |
RA | 8,753 | G→C | 72.3% | V172V (GTG→GTC) | talB → | transaldolase B |
RA | 8,762 | C→T | 73.7% | I175I (ATC→ATT) | talB → | transaldolase B |
RA | 8,771 | T→C | 74.2% | F178F (TTT→TTC) | talB → | transaldolase B |
RA | 8,783 | T→C | 76.1% | I182I (ATT→ATC) | talB → | transaldolase B |
RA | 8,786 | T→C | 75.9% | L183L (CTT→CTC) | talB → | transaldolase B |
RA | 8,801 | G→C | 75.3% | A188A (GCG→GCC) | talB → | transaldolase B |
RA | 8,804 | T→C | 74.1% | N189N (AAT→AAC) | talB → | transaldolase B |
RA | 8,810 | T→C | 76.6% | D191D (GAT→GAC) | talB → | transaldolase B |
RA | 8,825 | T→A | 76.4% | A196A (GCT→GCA) | talB → | transaldolase B |
RA | 8,852 | T→C | 75.1% | S205S (TCT→TCC) | talB → | transaldolase B |
RA | 8,855 | A→C | 74.4% | V206V (GTA→GTC) | talB → | transaldolase B |
RA | 8,856 | T→A | 73.7% | S207T (TCT→ACT) ‡ | talB → | transaldolase B |
RA | 8,857 | C→G | 73.7% | S207C (TCT→TGT) ‡ | talB → | transaldolase B |
RA | 8,858 | T→C | 74.1% | S207S (TCT→TCC) ‡ | talB → | transaldolase B |
RA | 8,868 | C→G | 76.4% | Q211E (CAG→GAG) | talB → | transaldolase B |
RA | 8,873 | C→T | 75.8% | Y212Y (TAC→TAT) | talB → | transaldolase B |
RA | 8,879 | A→G | 74.6% | K214K (AAA→AAG) | talB → | transaldolase B |
RA | 8,880 | G→C | 73.4% | E215Q (GAG→CAG) | talB → | transaldolase B |
RA | 8,888 | T→C | 74.0% | G217G (GGT→GGC) | talB → | transaldolase B |
RA | 8,900 | G→C | 70.7% | V221V (GTG→GTC) | talB → | transaldolase B |
RA | 8,903 | T→G | 70.6% | V222V (GTT→GTG) | talB → | transaldolase B |
RA | 8,925 | A→G | 65.6% | I230V (ATC→GTC) ‡ | talB → | transaldolase B |
RA | 8,927 | C→T | 65.9% | I230I (ATC→ATT) ‡ | talB → | transaldolase B |
RA | 8,948 | A→T | 64.4% | A237A (GCA→GCT) | talB → | transaldolase B |
RA | 8,954 | C→T | 65.3% | C239C (TGC→TGT) | talB → | transaldolase B |
RA | 8,960 | T→C | 65.9% | R241R (CGT→CGC) | talB → | transaldolase B |
RA | 8,972 | A→C | 60.8% | A245A (GCA→GCC) | talB → | transaldolase B |
RA | 8,978 | A→G | 59.5% | A247A (GCA→GCG) | talB → | transaldolase B |
RA | 8,994 | G→T | 60.5% | A253S (GCG→TCG) ‡ | talB → | transaldolase B |
RA | 8,996 | G→C | 61.4% | A253A (GCG→GCC) ‡ | talB → | transaldolase B |
RA | 8,999 | G→A | 61.4% | E254E (GAG→GAA) | talB → | transaldolase B |
RA | 9,008 | G→C | 59.1% | G257G (GGG→GGC) | talB → | transaldolase B |
RA | 9,011 | T→C | 58.4% | A258A (GCT→GCC) | talB → | transaldolase B |
RA | 9,012 | A→G | 57.7% | I259V (ATC→GTC) ‡ | talB → | transaldolase B |
RA | 9,014 | C→T | 56.8% | I259I (ATC→ATT) ‡ | talB → | transaldolase B |
RA | 9,017 | A→G | 57.0% | E260E (GAA→GAG) | talB → | transaldolase B |
RA | 9,023 | A→G | 57.6% | K262K (AAA→AAG) | talB → | transaldolase B |
RA | 9,027 | T→G | 54.6% | S264A (TCT→GCT) ‡ | talB → | transaldolase B |
RA | 9,028 | C→T | 54.3% | S264F (TCT→TTT) ‡ | talB → | transaldolase B |
RA | 9,029 | T→A | 55.3% | S264S (TCT→TCA) ‡ | talB → | transaldolase B |
RA | 9,032 | C→T | 55.9% | Y265Y (TAC→TAT) | talB → | transaldolase B |
RA | 9,038 | C→T | 56.8% | G267G (GGC→GGT) | talB → | transaldolase B |
RA | 9,058 | C→A | 62.0% | A274E (GCG→GAG) | talB → | transaldolase B |
RA | 9,065 | C→T | 61.2% | I276I (ATC→ATT) | talB → | transaldolase B |
RA | 9,068 | T→C | 60.0% | T277T (ACT→ACC) | talB → | transaldolase B |
RA | 9,071 | G→A | 59.8% | E278E (GAG→GAA) | talB → | transaldolase B |
RA | 9,074 | C→T | 58.7% | S279S (TCC→TCT) | talB → | transaldolase B |
RA | 9,092 | C→T | 54.9% | H285H (CAC→CAT) | talB → | transaldolase B |
RA | 9,104 | A→G | 52.8% | P289P (CCA→CCG) | talB → | transaldolase B |
RA | 9,110 | A→G | 50.7% | A291A (GCA→GCG) | talB → | transaldolase B |
RA | 9,116 | T→C | 49.3% | D293D (GAT→GAC) | talB → | transaldolase B |
RA | 9,146 | T→G | 38.0% | A303A (GCT→GCG) | talB → | transaldolase B |
RA | 9,149 | T→C | 32.7% | I304I (ATT→ATC) | talB → | transaldolase B |
RA | 9,178 | G→A | 25.5% | G314D (GGC→GAC) | talB → | transaldolase B |
RA | 9,182 | T→A | 23.6% | D315E (GAT→GAA) | talB → | transaldolase B |
RA | 360,147 | G→C | 20.9% | intergenic (‑81/+514) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,181 | G→C | 15.2% | 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 | 56.5% | coding (380/1110 nt) | frmA ← | alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase |
RA | 684,503:1 | +A | 22.2% | intergenic (‑34/+296) | insH1 ← / ← lnt | IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase |
JC JC | 982,570 | IS5 (–) +4 bp | 57.0% | intergenic (‑132/+468) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
RA | 1,005,859 | G→A | 30.6% | G147E (GGG→GAG) | uup → | putative transporter subunit of ABC superfamily: ATP‑binding component |
RA | 1,230,349 | T→C | 51.4% | intergenic (‑176/‑45) | nhaB ← / → fadR | sodium:proton antiporter/fatty acid metabolism regulon transcriptional regulator |
JC JC | 1,254,388 | IS5 (+) +4 bp | 29.2% | coding (142‑145/279 nt) | ychH → | DUF2583 family putative inner membrane protein |
RA | 1,484,009 | T→C | 48.2% | pseudogene (213/252 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
RA | 1,484,072 | G→A | 48.1% | 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 | 67.0% | intergenic (‑47/‑142) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
RA | 1,551,071 | C→T | 12.4% | L64F (CTT→TTT) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
RA | 1,551,091 | A→G | 7.1% | E70E (GAA→GAG) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
RA | 1,551,105 | C→A | 7.9% | P75Q (CCA→CAA) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
RA | 1,551,113 | A→T | 6.1% | I78F (ATT→TTT) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
RA | 1,551,119 | A→C | 15.7% | T80P (ACC→CCC) | osmC → | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
RA | 1,555,008 | T→C | 8.8% | D60G (GAC→GGC) | ddpB ← | D‑ala‑D‑ala transporter subunit |
RA | 1,555,013 | T→C | 10.9% | G58G (GGA→GGG) | ddpB ← | D‑ala‑D‑ala transporter subunit |
RA | 1,555,047 | T→C | 6.8% | D47G (GAT→GGT) | ddpB ← | D‑ala‑D‑ala transporter subunit |
RA | 1,555,059 | T→C | 8.7% | D43G (GAC→GGC) | ddpB ← | D‑ala‑D‑ala transporter subunit |
RA | 1,930,220 | C→G | 24.4% | 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 |
RA | 2,033,606 | G→C | 15.1% | P216P (CCG→CCC) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
JC | 2,066,645 | Δ18 bp | 23.7% | 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 | 2,145,108 | G→A | 19.6% | R148K (AGA→AAA) | yegJ → | uncharacterized protein |
RA | 2,145,170 | G→T | 35.1% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
RA | 3,001,588 | G→A | 5.9% | V240V (GTG→GTA) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
RA | 3,074,446 | A→G | 5.5% | D183D (GAT→GAC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,454 | A→C | 8.2% | F181V (TTC→GTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,455 | T→G | 8.1% | A180A (GCA→GCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,467 | A→G | 12.1% | G176G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,473 | C→T | 12.4% | K174K (AAG→AAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,478 | G→T | 12.3% | L173M (CTG→ATG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,481 | T→A | 12.1% | T172S (ACG→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,482 | A→G | 12.8% | G171G (GGT→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,485 | C→T | 12.9% | A170A (GCG→GCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,490 | G→A | 13.3% | L169L (CTG→TTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,491 | A→T | 13.3% | S168S (TCT→TCA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,498 | A→G | 13.3% | V166A (GTT→GCT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,503 | G→A | 15.2% | H164H (CAC→CAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,506 | G→C | 15.5% | S163S (TCC→TCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,521 | C→T | 20.8% | M158I (ATG→ATA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,523 | T→A | 20.8% | M158L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,538 | T→G | 26.2% | M153L (ATG→CTG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,563 | A→G | 26.1% | I144I (ATT→ATC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,566 | G→T | 25.4% | D143E (GAC→GAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,575 | C→G | 26.0% | P140P (CCG→CCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,578 | A→G | 26.3% | R139R (CGT→CGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,584 | A→G | 21.9% | F137F (TTT→TTC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,587 | C→T | 21.8% | Q136Q (CAG→CAA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,590 | C→G | 22.0% | A135A (GCG→GCC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,591 | G→C | 21.3% | A135G (GCG→GGG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,601 | T→C | 16.5% | T132A (ACG→GCG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,602 | T→G | 15.3% | K131N (AAA→AAC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,603 | T→C | 16.2% | K131R (AAA→AGA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,604 | T→G | 16.4% | K131Q (AAA→CAA) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,608 | T→G | 15.2% | 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 | 15.9% | M126I (ATG→ATC) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,619 | T→A | 16.5% | M126L (ATG→TTG) ‡ | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,623 | G→C | 16.7% | 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 | 16.3% | N122N (AAC→AAT) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,634 | C→T | 14.9% | 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 | 15.3% | 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 | 13.0% | 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 | 13.3% | G114G (GGT→GGA) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,659 | G→C | 8.4% | T112T (ACC→ACG) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
RA | 3,074,662 | G→C | 8.2% | 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 |
JC JC | 4,053,617 | IS4 (+) +12 bp | 65.7% | 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] | |
MC JC | 4,303,167 | Δ450 bp | 100% | coding (1‑450/450 nt) | rpiB → | ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase |
JC | 4,629,755 | +TTCAT | 23.7% | coding (369/717 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 | 1308881 | 1308955 | 75 | 35 [34] | [0] 75 | [ompW] | [ompW] |
* | * | ÷ | CP009273 | 1857028 | 1858030 | 1003 | 71 [0] | [0] 65 | [gapA] | [gapA] |
* | * | ÷ | CP009273 | 3099970 | 3100016 | 47 | 36 [34] | [32] 36 | nupG | nucleoside transporter |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | CP009273 | 19796 = | NA (NA) | 5 (0.070) | 5/276 | NT | 7.5% | noncoding (768/768 nt) | IS1 | repeat region |
? | CP009273 | = 2461501 | 62 (0.900) | coding (168/363 nt) | gtrA | CPS‑53 (KpLE1) prophage; bactoprenol‑linked glucose translocase (flippase) | |||||
* | ? | CP009273 | 360104 = | 61 (0.890) | 51 (0.740) | 49/276 | NT | 45.5% | 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 | 454243 = | 50 (0.730) | 13 (0.190) | 13/270 | NT | 21.0% | intergenic (+87/‑101) | 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 | 454243 = | 50 (0.730) | 4 (0.060) | 4/270 | NT | 7.6% | 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 | = 454255 | 49 (0.710) | 22 (0.330) | 21/268 | NT | 31.6% | 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) | 34 (0.500) | 30/270 | NT | 53.7% | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex |
? | CP009273 | 1297568 = | 30 (0.440) | coding (413/921 nt) | oppB | oligopeptide transporter subunit | |||||
* | ? | CP009273 | 1203246 = | 45 (0.650) | 10 (0.160) | 9/244 | NT | 18.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | 1205075 = | 47 (0.770) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1203261 | 46 (0.670) | 11 (0.180) | 11/244 | NT | 20.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | = 1205058 | 47 (0.770) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1297580 | 33 (0.480) | 24 (0.360) | 21/268 | NT | 42.8% | coding (425/921 nt) | oppB | oligopeptide transporter subunit |
? | CP009273 | 2507756 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
* | ? | CP009273 | 1308956 = | 0 (0.000) | 34 (0.900) +62 bp |
32/152 | NT | 83.7% | intergenic (+41/+19) | ompW/yciE | outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein |
? | CP009273 | = 4161777 | 24 (0.350) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding | |||||
* | ? | CP009273 | = 1463497 | NA (NA) | 10 (0.150) | 10/272 | NT | 16.4% | noncoding (1/1331 nt) | IS2 | repeat region |
? | CP009273 | 1747090 = | 51 (0.750) | coding (998/2103 nt) | ydhV | putative oxidoreductase subunit | |||||
* | ? | CP009273 | 1483968 = | NA (NA) | 60 (0.870) | 54/276 | 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 | 84 (1.220) | 39 (0.920) +53 bp |
35/170 | NT | 60.1% | 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 = | 86 (1.250) | 840 (12.290) | 253/274 | NT | 91.4% | coding (120/432 nt) | osmC | lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
? | CP009273 | = 1558191 | 72 (1.050) | coding (1800/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||
* | ? | CP009273 | = 1645803 | NA (NA) | 14 (0.210) | 14/272 | NT | 21.5% | intergenic (+9/‑5) | 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 | = 1747096 | 52 (0.760) | coding (992/2103 nt) | ydhV | putative oxidoreductase subunit | |||||
* | ? | CP009273 | 2382388 = | 66 (0.960) | 8 (0.120) | 8/274 | NT | 10.9% | coding (275/423 nt) | yfbO | uncharacterized protein |
? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
* | ? | CP009273 | 3052022 = | 9 (0.130) | 2633 (38.820) +AG |
200/272 | NT | 99.7% | 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 = | 63 (0.920) | 126 (1.830) | 100/276 | NT | 66.7% | 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) | 69 (1.000) | 62/276 | 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 (0.940) | 58/276 | 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 = | 58 (0.840) | 5 (0.080) | 5/258 | NT | 7.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
? | CP009273 | 4532813 = | 71 (1.100) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |