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 = 45425549 (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 = 604803NA (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 = 120326146 (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 = 129758033 (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 = 1463497NA (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 = 148508584 (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 = 1645803NA (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 = 3180785NA (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)