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 | annotation | gene | description |
| RA | 5,382 | A→G | H50R (CAC→CGC) | b0005 → | hypothetical protein |
| RA | 34,711 | A→G | intergenic (+16/+70) | caiF → / ← caiE | transcriptional regulator of cai operon/CaiE |
| RA | 46,567 | G→A | C254Y (TGC→TAC) | yaaU → | putative transport protein |
| RA | 50,798 | A→G | V142A (GTG→GCG) | apaH ← | diadenosine tetraphosphatase |
| RA | 56,445 | T→C | D222G (GAC→GGC) | imp ← | organic solvent tolerance |
| RA | 66,528 | T→C | Q8R (CAG→CGG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase |
| MC JC | 66,533 | 3540 bp→27 bp | [araD]–araB | [araD], araA, araB | |
| RA | 70,289 | G→T | intergenic (‑241/‑98) | araB ← / → araC | L‑ribulokinase/transcriptional regulator for ara operon |
| RA | 78,003 | A→C | E128A (GAG→GCG) | yabM → | putative transport protein |
| RA | 78,217 | A→G | E199E (GAA→GAG) | yabM → | putative transport protein |
| RA | 106,897 | T→A | L114Q (CTG→CAG) | lpxC → | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase |
| RA | 174,640 | A→G | R81R (CGT→CGC) | hemL ← | glutamate‑1‑semialdehyde aminotransferase |
| RA | 188,475 | T→C | Q59R (CAG→CGG) | glnD ← | protein PII |
| RA | 203,775 | T→C | V143A (GTG→GCG) | lpxB → | tetraacyldisaccharide‑1‑P |
| RA | 234,824 | G→A | P9P (CCG→CCA) | yafS → | hypothetical protein |
| RA | 383,887 | A→G | intergenic (‑47/‑512) | yaiS ← / → tauA | hypothetical protein/TauA |
| RA | 448,554 | A→G | Y438H (TAC→CAC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 485,747 | A→G | intergenic (+115/‑13) | acrR → / → aefA | acrAB operon repressor/putative alpha helix protein |
| RA | 502,653 | C→T | intergenic (‑191/+47) | ybaL ← / ← fsr | putative transport protein/fosmidomycin resistance protein |
| RA | 515,579 | T→C | I146T (ATC→ACC) | ybbL → | putative ATP‑binding component of a transport system |
| RA | 547,694 | A→G | E38E (GAA→GAG) | b4507 → | hypothetical protein |
| RA | 547,835 | +G | coding (255/261 nt) | b4507 → | hypothetical protein |
| RA | 560,123 | A→G | T402A (ACG→GCG) | sfmD → | putative outer membrane protein |
| RA | 561,644 | A→G | Y27C (TAT→TGT) | sfmH → | involved in fimbrial asembly |
| RA | 580,425 | T→A | G123G (GGT→GGA) | nohB → | bacteriophage DNA packaging protein |
| RA | 580,429 | A→G | I125V (ATT→GTT) | nohB → | bacteriophage DNA packaging protein |
| RA | 580,509 | G→C | L151L (CTG→CTC) | nohB → | bacteriophage DNA packaging protein |
| RA | 596,240 | G→A | intergenic (+44/‑114) | ylcB → / → ylcC | putative resistance protein/hypothetical protein |
| RA | 620,296 | A→G | V39A (GTA→GCA) | fepG ← | FepG |
| RA | 677,120 | G→A | A161A (GCG→GCA) | ybeS → | hypothetical protein |
| RA | 690,574 | A→G | V145A (GTT→GCT) | ybeX ← | putative transport protein |
| RA | 693,605 | C→T | G192S (GGC→AGC) | yleA ← | hypothetical protein |
| RA | 704,236 | T→C | L357S (TTG→TCG) | nagE → | PTS system, N‑acetylglucosamine‑specific enzyme IIABC |
| RA | 757,511 | A→C | A200A (GCA→GCC) | sdhB → | succinate dehydrogenase iron sulfur protein |
| RA | 764,635 | T→C | Q155R (CAG→CGG) | farR ← | FarR |
| RA | 778,625 | T→C | R112R (CGT→CGC) | pal → | peptidoglycan‑associated lipoprotein |
| RA | 806,926 | T→C | L69L (TTA→TTG) | ybhB ← | hypothetical protein |
| RA | 817,441 | A→G | Y55C (TAC→TGC) | moaB → | molybdopterin biosynthesis protein B |
| RA | 832,964 | T→C | H224H (CAT→CAC) | dinG → | putative ATP‑dependent helicase |
| RA | 857,347 | A→G | V313A (GTA→GCA) | ybiU ← | hypothetical protein |
| RA | 891,914 | T→C | L242P (CTG→CCG) | rimK → | ribosomal protein S6 modification protein |
| RA | 910,552 | A→G | R274R (CGT→CGC) | b0872 ← | hypothetical protein |
| RA | 1,015,425 | A→T | L90Q (CTG→CAG) | fabA ← | beta‑hydroxydecanoyl thioester dehydrase |
| RA | 1,056,041 | A→G | E186E (GAA→GAG) | torT → | TorT |
| RA | 1,237,202 | A→G | T137A (ACG→GCG) | dadA → | D‑amino acid dehydrogenase subunit |
| RA | 1,251,414 | G→A | A379T (GCA→ACA) | b1201 → | putative sensor‑type regulator |
| RA | 1,302,782 | A→G | N2S (AAC→AGC) | oppD → | OppD |
| RA | 1,322,824 | T→C | S19P (TCT→CCT) | yciQ → | hypothetical protein |
| RA | 1,335,418 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydrase 1 |
| RA | 1,447,942 | C→T | V478I (GTC→ATC) | tynA ← | copper amine oxidase |
| RA | 1,607,710 | A→G | L332P (CTT→CCT) | uxaB ← | altronate oxidoreductase |
| RA | 1,634,017 | A→T | I125V (ATT→GTA) | nohA ← | NohA |
| RA | 1,634,019 | T→C | I125V (ATT→GTA) | nohA ← | NohA |
| RA | 1,634,023 | A→T | G123G (GGT→GGA) | nohA ← | NohA |
| RA | 1,643,412 | T→C | E82E (GAA→GAG) | relE ← | hypothetical protein |
| RA | 1,650,355 | T→C | F274L (TTC→CTC) | b1579 → | putative transposase |
| RA | 1,652,626 | T→C | E180E (GAA→GAG) | rspA ← | starvation sensing protein |
| RA | 1,672,424 | T→C | L163P (CTC→CCC) | b1601 → | putative transport protein |
| RA | 1,678,790 | T→C | S404P (TCT→CCT) | b1605 → | putative arginine/ornithine antiporter |
| RA | 1,690,632 | A→G | Y78H (TAT→CAT) | uidC ← | membrane‑associated protein |
| RA | 1,692,491 | G→A | R535R (CGC→CGT) | uidA ← | beta‑D‑glucuronidase |
| RA | 1,718,191 | A→G | T98A (ACT→GCT) | slyB → | putative outer membrane protein |
| RA | 1,722,918 | T→A | N247Y (AAC→TAC) | b1647 ← | hypothetical protein |
| RA | 1,729,429 | G→A | S773S (TCG→TCA) | lhr → | Lhr |
| RA | 1,739,051 | A→G | M373V (ATG→GTG) | ydhC → | putative transport protein |
| RA | 1,741,574 | 2 bp→GA | coding (94‑95/1374 nt) | ydhE → | putative transport protein |
| RA | 1,773,032 | G→A | G108D (GGC→GAC) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,812,482 | T→C | F198L (TTC→CTC) | katE → | catalase |
| RA | 1,815,038 | T→C | Q41R (CAG→CGG) | ydjC ← | hypothetical protein |
| RA | 1,830,970 | T→C | R173R (CGT→CGC) | xthA → | exonuclease III |
| RA | 1,860,370 | T→C | E28E (GAA→GAG) | yeaA ← | hypothetical protein |
| RA | 1,897,431 | T→C | H327H (CAT→CAC) | b1815 → | hypothetical protein |
| RA | 1,949,344 | G→A | Q174Q (CAG→CAA) | yecD → | hypothetical protein |
| RA | 1,949,356 | T→C | S178S (AGT→AGC) | yecD → | hypothetical protein |
| RA | 1,949,359 | C→T | I179I (ATC→ATT) | yecD → | hypothetical protein |
| RA | 1,949,362 | C→T | N180N (AAC→AAT) | yecD → | hypothetical protein |
| RA | 1,949,410 | 2 bp→TC | coding (588‑589/600 nt) | yecD → | hypothetical protein |
| RA | 1,949,436 | A→G | L6L (CTA→CTG) | yecE → | hypothetical protein |
| MC JC | 1,976,527 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 1,980,940 | +C | coding (1/363 nt) coding (627/627 nt) |
araH ← araH ← |
ABC‑type arabinose transport system permease component ABC‑type arabinose transport system permease component |
| RA | 2,008,480 | +A | coding (637/654 nt) | yedK → | hypothetical protein |
| RA | 2,015,142 | T→C | S189S (AGT→AGC) | fliI → | flagellum‑specific ATP synthase |
| RA | 2,025,101 | T→C | A318A (GCA→GCG) | b1956 ← | hypothetical protein |
| RA | 2,043,272 | A→G | S130G (AGT→GGT) | b1978 → | hypothetical protein |
| RA | 2,072,030 | T→A | C824S (TGC→AGC) | b2000 → | outer membrane fluffing protein |
| RA | 2,118,886 | T→C | T231A (ACC→GCC) | wcaJ ← | putative colanic acid biosynthsis UDP‑glucose lipid carrier transferase |
| RA | 2,216,746 | G→C | S252S (TCC→TCG) | yehZ ← | putative transport system permease protein |
| RA | 2,313,133 | T→C | P542P (CCT→CCC) | yojN → | putative 2‑component sensor protein |
| RA | 2,319,081 | G→A | R340H (CGT→CAT) | atoS → | AtoS |
| RA | 2,402,412 | C→T | A74A (GCG→GCA) | nuoB ← | NADH dehydrogenase I chain B |
| RA | 2,429,483 | T→C | E65E (GAA→GAG) | dedD ← | putative lipoprotein |
| RA | 2,549,500 | T→C | T83A (ACG→GCG) | b2433 ← | hypothetical protein |
| RA | 2,563,580 | T→C | D442G (GAC→GGC) | b2451 ← | hypothetical protein |
| RA | 2,594,929 | T→C | D237G (GAC→GGC) | purC ← | phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| RA | 2,599,294 | T→C | V25A (GTG→GCG) | b2481 → | hydrogenase 4 Fe‑S subunit |
| RA | 2,623,346 | T→C | L71P (CTG→CCG) | ppx → | exopolyphosphatase |
| RA | 2,655,609 | G→C | R449R (CGC→CGG) | hscA ← | HscA |
| RA | 2,656,601 | T→C | T119A (ACG→GCG) | hscA ← | HscA |
| RA | 2,691,024 | A→T | F847Y (TTT→TAT) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,727,394 | T→C | noncoding (71/76 nt) | gltW ← | tRNA‑Sec |
| RA | 2,729,373 | +C | intergenic (‑195/+247) | rrsG ← / ← clpB | 16S ribosomal RNA/ClpB |
| RA | 2,747,389 | Δ1 bp | coding (572/591 nt) | b4540 → | hypothetical protein |
| RA | 2,748,385 | A→G | D115D (GAT→GAC) | grpE ← | GrpE |
| RA | 2,751,091 | G→C | A426P (GCT→CCT) | recN → | RecN |
| RA | 2,764,178 | G→A | L80L (CTG→CTA) | yfjN → | putative cell division protein |
| RA | 2,766,382 | C→G | P218A (CCC→GCC) | b2632 → | putative GTP‑binding protein |
| RA | 2,766,423 | G→A | R231R (CGG→CGA) | b2632 → | putative GTP‑binding protein |
| RA | 2,766,427 | 2 bp→AC | coding (697‑698/864 nt) | b2632 → | putative GTP‑binding protein |
| RA | 2,766,473 | A→G | D248G (GAT→GGT) | b2632 → | putative GTP‑binding protein |
| RA | 2,766,475 | A→G | T249A (ACC→GCC) | b2632 → | putative GTP‑binding protein |
| RA | 2,781,020 | +G | intergenic (‑144/+65) | ypjA ← / ← b2648 | putative ATP‑binding component of a transport system/hypothetical protein |
| RA | 2,781,027 | C→G | intergenic (‑151/+58) | ypjA ← / ← b2648 | putative ATP‑binding component of a transport system/hypothetical protein |
| RA | 2,781,134 | T→C | D32G (GAC→GGC) | b2648 ← | hypothetical protein |
| RA | 2,785,180 | Δ1 bp | coding (413/495 nt) | b2655 → | hypothetical protein |
| RA | 2,803,648 | T→C | S271S (AGT→AGC) | proV → | ATP‑binding component of transport system for glycine, betaine and proline |
| RA | 2,812,859 | Δ1 bp | intergenic (‑105/+46) | ygaG ← / ← gshA | hypothetical protein/gamma‑glutamate‑cysteine ligase |
| RA | 2,819,446 | G→C | G196G (GGC→GGG) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,820,144 | Δ1 bp | intergenic (+24/+18) | b4542 → / ← oraA | hypothetical protein/OraA |
| RA | 2,823,915 | A→G | K21E (AAG→GAG) | srlA → | PTS system, glucitol/sorbitol‑specific IIC component |
| RA | 2,824,797 | T→C | F128S (TTT→TCT) | srlE → | PTS system glucitol/sorbitol‑specific enzyme IIBC component |
| RA | 2,825,102 | T→C | F230L (TTC→CTC) | srlE → | PTS system glucitol/sorbitol‑specific enzyme IIBC component |
| RA | 2,838,044 | +G | coding (498/1458 nt) | ascF → | PTS system enzyme IIBC |
| RA | 2,838,055 | Δ1 bp | coding (509/1458 nt) | ascF → | PTS system enzyme IIBC |
| RA | 2,842,033 | G→T | R67R (CGC→CGA) | hycG ← | hydrogenase activity |
| RA | 2,857,315 | C→T | Q734* (CAG→TAG) | mutS → | MutS |
| JC | 2,875,936 | Δ61 bp | intergenic (+295/+596) | iap → / ← ygbF | Iap/hypothetical protein |
| RA | 2,896,819 | +C | coding (622/657 nt) | ygcU ← | putative oxidoreductase subunit |
| RA | 2,897,800 | A→G | Y166H (TAT→CAT) | b2774 ← | putative oxidoreductase |
| RA | 2,908,853 | T→C | G87G (GGA→GGG) | chpA ← | ChpA |
| RA | 2,977,924 | A→G | L294L (TTA→TTG) | lysR → | LysR |
| RA | 3,005,399 | +C | coding (1044/1092 nt) | ygeW → | putative carbamoyl transferase |
| RA | 3,025,676 | +C | coding (535/570 nt) | ygfQ → | hypothetical protein |
| RA | 3,059,022 | T→C | G51G (GGT→GGC) | sbm → | methylmalonyl‑CoA mutase |
| RA | 3,075,220 | (T)5→6 | coding (256/357 nt) | yggP ← | hypothetical protein |
| RA | 3,077,514 | Δ1 bp | intergenic (‑165/+149) | cmtB ← / ← tktA | PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme |
| RA | 3,077,640 | +G | intergenic (‑291/+23) | cmtB ← / ← tktA | PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme |
| RA | 3,077,905 | A→G | S584P (TCG→CCG) | tktA ← | transketolase 1 isozyme |
| RA | 3,078,245 | C→G | G470G (GGG→GGC) | tktA ← | transketolase 1 isozyme |
| RA | 3,099,661 | (A)5→6 | intergenic (‑19/+164) | yggN ← / ← b2959 | hypothetical protein/hypothetical protein |
| RA | 3,107,469 | +C | intergenic (‑296/‑101) | b2965 ← / → yqgA | ornithine decarboxylase isozyme/putative transport protein |
| RA | 3,108,438 | C→A | noncoding (56/76 nt) | pheV → | tRNA‑Phe |
| RA | 3,115,116 | +C | coding (2013/2028 nt) | b2974 ← | putative endoglucanase |
| RA | 3,123,585 | +G | coding (953/2286 nt) | glcF ← | glycolate oxidase iron‑sulfur subunit |
| RA | 3,130,334 | A→G | V30V (GTT→GTC) | b2983 ← | hypothetical protein |
| RA | 3,142,022 | A→G | V53A (GTG→GCG) | hybB ← | putative cytochrome Ni/Fe component of hydrogenase‑2 |
| RA | 3,152,247 | +C | intergenic (+10/+29) | yghB → / ← yqhC | hypothetical protein/putative ARAC‑type regulatory protein |
| MC JC | 3,156,257 | (CCA)2→1 | coding (594‑596/930 nt) | yqhG → | hypothetical protein |
| RA | 3,158,202 | +C | coding (961/975 nt) | ygiRQ ← | Fe‑S oxidoreductase |
| RA | 3,166,935 | 2 bp→CG | coding (312‑313/483 nt) | b3023 ← | hypothetical protein |
| RA | 3,185,776 | T→C | F121L (TTC→CTC) | yqiG → | putative membrane protein |
| RA | 3,185,807 | T→C | F131S (TTT→TCT) | yqiG → | putative membrane protein |
| RA | 3,197,191 | T→C | Q31R (CAG→CGG) | glnE ← | GlnE |
| RA | 3,221,097 | 2 bp→GC | coding (824‑825/3093 nt) | b3076 → | evolved beta‑D‑galactosidase alpha subunit |
| RA | 3,222,944 | 4 bp→AGCA | coding (2671‑2674/3093 nt) | b3076 → | evolved beta‑D‑galactosidase alpha subunit |
| RA | 3,224,879 | Δ1 bp | coding (1005/1434 nt) | ygjI → | putative oxidoreductase |
| RA | 3,224,926 | +C | coding (1052/1434 nt) | ygjI → | putative oxidoreductase |
| RA | 3,236,177 | Δ1 bp | intergenic (+239/‑45) | ygjR → / → ygjT | hypothetical protein/putative transport protein |
| RA | 3,236,735 | +C | coding (514/966 nt) | ygjT → | putative transport protein |
| RA | 3,236,758 | Δ1 bp | coding (537/966 nt) | ygjT → | putative transport protein |
| RA | 3,237,242 | +C | intergenic (+55/‑342) | ygjT → / → ygjU | putative transport protein/putative transport protein |
| RA | 3,237,247 | +C | intergenic (+60/‑337) | ygjT → / → ygjU | putative transport protein/putative transport protein |
| RA | 3,253,742 | Δ1 bp | coding (551/552 nt) | yhaNM ← | hypothetical protein |
| RA | 3,255,594 | Δ1 bp | coding (4/1278 nt) | yhaO ← | putative transport system permease protein |
| RA | 3,255,616 | Δ1 bp | intergenic (‑19/+312) | yhaO ← / ← yhaP | putative transport system permease protein/putative L‑serine dehydratase |
| RA | 3,256,893 | +C | coding (405/423 nt) | yhaQ ← | putative L‑serine dehydratase |
| RA | 3,257,838 | +G | coding (2222/2241 nt) | tdcE ← | putative formate acetyltransferase 3 |
| RA | 3,279,197 | A→C | R145S (AGA→AGC) | agaA → | putative N‑acetylgalactosamine‑6‑phosphate deacetylase |
| RA | 3,298,112 | T→C | G96G (GGA→GGG) | yhbS ← | hypothetical protein |
| RA | 3,333,863 | A→G | R91R (CGT→CGC) | murA ← | UDP‑N‑glucosamine 1‑carboxyvinyltransferase |
| RA | 3,352,254 | 2 bp→GC | intergenic (‑569/‑12) | yhcC ← / → gltB | hypothetical protein/glutamate synthase large subunit |
| RA | 3,374,875 | T→G | T61P (ACC→CCC) | sspA ← | stringent starvation protein A |
| RA | 3,389,812 | Δ1 bp | intergenic (‑149/+4151) | tldD ← / ← cafA | TldD/CafA |
| RA | 3,393,106 | Δ1 bp | intergenic (‑3443/+857) | tldD ← / ← cafA | TldD/CafA |
| RA | 3,418,840 | +G | coding (1070/1089 nt) | b3269 → | putative transport system permease protein |
| RA | 3,421,120 | Δ1 bp | noncoding (60/121 nt) | rrfF ← | 5S ribosomal RNA |
| RA | 3,429,527 | Δ1 bp | coding (40/510 nt) | yrdD ← | putative DNA topoisomerase |
| RA | 3,430,453 | +C | coding (745/747 nt) | smf ← | putative Rossmann‑fold nucleotide‑binding protein |
| RA | 3,453,670 | T→C | T152T (ACT→ACC) | yheE → | YheE |
| RA | 3,472,030 | G→A | R54C (CGT→TGT) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,500,309 | Δ1 bp | coding (333/363 nt) | b3372 → | hypothetical protein |
| RA | 3,509,958 | Δ1 bp | intergenic (‑195/+314) | yhfZ ← / ← trpS | hypothetical protein/tryptophan tRNA synthetase |
| RA | 3,510,121 | +G | intergenic (‑358/+151) | yhfZ ← / ← trpS | hypothetical protein/tryptophan tRNA synthetase |
| RA | 3,537,252 | C→T | P744S (CCG→TCG) | b3407 → | hypothetical protein |
| RA | 3,537,405 | +GC | intergenic (+61/‑394) | b3407 → / → feoA | hypothetical protein/ferrous iron transport protein A |
| RA | 3,544,357 | +G | coding (163/1314 nt) | gntT → | gluconate permease |
| RA | 3,544,360 | +G | coding (166/1314 nt) | gntT → | gluconate permease |
| RA | 3,544,363 | +C | coding (169/1314 nt) | gntT → | gluconate permease |
| RA | 3,548,005 | C→T | G701D (GGT→GAT) | malP ← | maltodextrin phosphorylase |
| RA | 3,554,088 | +C | coding (2/624 nt) | yhgKJ ← | RNA phosphage cyclase |
| RA | 3,554,113 | Δ1 bp | coding (372/396 nt) | yhgKJ ← | RNA phosphage cyclase |
| RA | 3,554,118 | +C | coding (367/396 nt) | yhgKJ ← | RNA phosphage cyclase |
| RA | 3,558,932 | 2 bp→GC | coding (153‑154/831 nt) | glpG ← | GlpG |
| RA | 3,573,700 | +C | intergenic (+403/+997) | yhgN → / ← gntK | hypothetical protein/gluconokinase 2 |
| RA | 3,575,446 | +G | coding (912/942 nt) | gntR ← | GntR |
| RA | 3,585,834 | A→G | H339H (CAT→CAC) | ugpC ← | ATP‑binding component of sn‑glycerol 3‑phosphate transport system |
| RA | 3,627,142 | +G | intergenic (‑24/+23) | yhiH ← / ← yhiI | putative ATP‑binding component of a transport system, fragment 1/putative membrane protein |
| RA | 3,663,106 | A→G | L112P (CTA→CCA) | yhiX ← | putative ARAC‑type regulatory protein |
| RA | 3,686,775 | +T | intergenic (‑23/+9) | b3530 ← / ← yhjM | putative oxidoreductase subunit/putative endoglucanase |
| RA | 3,687,487 | T→C | Q135R (CAG→CGG) | yhjM ← | putative endoglucanase |
| RA | 3,703,602 | 2 bp→GC | intergenic (‑183/+124) | dppB ← / ← dppA | dipeptide transport system permease protein 1/dipeptide transport protein |
| RA | 3,714,436 | 2 bp→GC | coding (261‑262/660 nt) | yiaD → | putative outer membrane protein |
| RA | 3,734,264 | 2 bp→GC | coding (542‑543/825 nt) | bax ← | putative ATP‑binding protein |
| RA | 3,736,298 | T→C | N391N (AAT→AAC) | malS → | alpha‑amylase |
| RA | 3,737,956 | 2 bp→CG | coding (623‑624/1254 nt) | avtA → | alanine‑alpha‑ketoisovalerate transaminase |
| RA | 3,743,603 | Δ1 bp | coding (1171/1275 nt) | yiaN → | putative membrane protein |
| RA | 3,754,310 | C→A | R382M (AGG→ATG) | yiaY ← | putative oxidoreductase |
| JC | 3,754,317 | +GCG | coding (1138/1149 nt) | yiaY ← | putative oxidoreductase |
| RA | 3,765,203 | A→T | Q119L (CAG→CTG) | yibJ → | hypothetical protein |
| RA | 3,765,234 | G→A | G129G (GGG→GGA) | yibJ → | hypothetical protein |
| RA | 3,782,932 | T→C | Y16H (TAT→CAT) | yibO → | putative 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,790,609 | G→A | D239D (GAC→GAT) | htrL ← | HtrL |
| RA | 3,810,753 | T→C | A132A (GCT→GCC) | b3639 → | Dfp |
| RA | 3,870,631 | Δ1 bp | coding (610/1764 nt) | dgoA ← | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase |
| RA | 3,870,765 | +G | coding (476/1764 nt) | dgoA ← | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase |
| RA | 3,870,876 | Δ1 bp | coding (365/1764 nt) | dgoA ← | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase |
| RA | 3,872,450 | +G | coding (338/387 nt) | yidW ← | regulator protein for dgo operon |
| RA | 3,873,627 | Δ1 bp | coding (506/672 nt) | yidX → | putative replicase |
| RA | 3,876,595 | G→C | P385A (CCG→GCG) | gyrB ← | DNA gyrase subunit B |
| RA | 3,881,483 | Δ1 bp | intergenic (‑126/‑482) | dnaA ← / → rpmH | DnaA/50S ribosomal subunit protein L34 |
| RA | 3,889,728 | C→T | A162V (GCG→GTG) | yidY → | putative transport protein |
| RA | 3,896,324 | +G | coding (698/711 nt) | b3718 ← | putative isomerase |
| RA | 3,905,202 | T→C | D2G (GAC→GGC) | phoU ← | PhoU |
| RA | 3,927,062 | +G | coding (2/1284 nt) coding (169/183 nt) |
yieM ← b4564 ← |
hypothetical protein hypothetical protein |
| RA | 3,928,669 | A→G | L18L (TTG→CTG) | yieN ← | putative 2‑component regulator |
| RA | 3,930,457 | Δ1 bp | coding (1515/1560 nt) | kup → | low affinity potassium transport system |
| RA | 3,930,568 | +G | intergenic (+66/‑373) | kup → / → rbsD | low affinity potassium transport system/RbsD |
| RA | 3,930,677 | +G | intergenic (+175/‑264) | kup → / → rbsD | low affinity potassium transport system/RbsD |
| RA | 3,932,295 | C→T | L298F (CTC→TTC) | rbsA → | ATP‑binding component of D‑ribose high‑affinity transport system |
| JC | 3,938,587 | +TGC | coding (220/546 nt) | yiePs ← | hypothetical protein |
| RA | 3,941,734 | Δ1 bp | noncoding (409/2906 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,944,244 | C→A | intergenic (+13/‑80) | rrlC → / → rrfC | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 3,944,676 | 2 bp→GC | intergenic (+20/+75) | trpT → / ← yifDA | tRNA‑Trp/transcription regulator |
| RA | 3,945,351 | +C | coding (1/600 nt) coding (240/240 nt) |
yifDA ← yifDA ← |
transcription regulator transcription regulator |
| RA | 3,948,087 | G→A | intergenic (+44/‑96) | ilvL → / → ilvG | ilvGEDA operon leader peptide/acetolactate synthase II large subunit |
| RA | 3,950,557 | 2 bp→GC | coding (451‑452/930 nt) | ilvE → | branched‑chain amino‑acid aminotransferase |
| RA | 3,951,166 | +C | coding (35/1818 nt) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,951,168 | +G | coding (37/1818 nt) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,951,478 | C→T | P116L (CCG→CTG) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,957,092 | +CC | intergenic (+26/+58) | ilvC → / ← ppiC | ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C |
| RA | 3,957,124 | +G | intergenic (+58/+26) | ilvC → / ← ppiC | ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C |
| RA | 3,957,548 | 1 bp→GG | intergenic (‑117/‑744) | ppiC ← / → rep | peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
| RA | 3,957,551 | +T | intergenic (‑120/‑741) | ppiC ← / → rep | peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
| RA | 3,957,560 | +C | intergenic (‑129/‑732) | ppiC ← / → rep | peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
| RA | 3,958,877 | 2 bp→CG | coding (586‑587/2022 nt) | rep → | rep helicase |
| RA | 3,959,281 | G→A | E330E (GAG→GAA) | rep → | rep helicase |
| RA | 3,960,578 | 2 bp→CG | coding (1266‑1267/1485 nt) | gppA ← | guanosine pentaphosphatase |
| RA | 3,961,588 | C→G | R86T (AGG→ACG) | gppA ← | guanosine pentaphosphatase |
| JC | 3,968,317 | +CGT | coding (612/1170 nt) | wecB → | UDP‑N‑acetyl glucosamine ‑2‑epimerase |
| RA | 3,969,103 | 2 bp→GC | coding (232‑233/1263 nt) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 3,971,075 | 2 bp→GC | coding (942‑943/1068 nt) | rffG → | dTDP‑glucose 4,6‑dehydratase |
| RA | 3,972,637 | 2 bp→GC | coding (430‑431/546 nt) | wecD → | hypothetical protein |
| RA | 3,975,313 | Δ1 bp | intergenic (+173/‑901) | wzxE → / → wecF | putative cytochrome/TDP‑Fuc4NAc:lipidII transferase |
| RA | 3,978,702 | C→T | S68F (TCC→TTC) | yifK → | putative amino acid/amine transport protein |
| RA | 3,979,535 | +G | coding (1036/1386 nt) | yifK → | putative amino acid/amine transport protein |
| RA | 3,979,546 | Δ1 bp | coding (1047/1386 nt) | yifK → | putative amino acid/amine transport protein |
| RA | 3,980,918 | 2 bp→CG | coding (348‑349/1236 nt) | aslB → | putative arylsulfatase regulator |
| RA | 3,987,586 | 2 bp→GC | coding (814‑815/963 nt) | hemC ← | porphobilinogen deaminase |
| RA | 3,987,822 | 2 bp→CG | coding (578‑579/963 nt) | hemC ← | porphobilinogen deaminase |
| RA | 3,998,290 | +G | coding (379/486 nt) | b4566 ← | hypothetical protein |
| RA | 4,001,421 | 2 bp→GC | coding (381‑382/903 nt) | rarD ← | hypothetical protein |
| RA | 4,001,486 | 2 bp→GC | coding (316‑317/903 nt) | rarD ← | hypothetical protein |
| RA | 4,001,717 | +C | coding (86/903 nt) | rarD ← | hypothetical protein |
| RA | 4,004,979 | +G | coding (1511/1833 nt) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,004,984 | +CG | coding (1516/1833 nt) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,005,601 | +C | coding (237/282 nt) | b4568 → | hypothetical protein |
| RA | 4,006,483 | +C | coding (183/207 nt) | b4554 ← | hypothetical protein |
| RA | 4,007,718 | 2 bp→CG | coding (943‑944/1023 nt) | pldB → | lysophospholipase L(2) |
| RA | 4,007,907 | +GG | intergenic (+109/‑11) | pldB → / → b4555 | lysophospholipase L(2)/hypothetical protein |
| RA | 4,008,375 | +A | coding (458/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,391 | +C | coding (474/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,393 | C→G | A159G (GCT→GGT) | b4555 → | hypothetical protein |
| RA | 4,008,400 | +GAAA | coding (483/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,404 | +G | coding (487/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,411 | +C | coding (494/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,421 | +T | coding (504/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,429 | +TG | coding (512/516 nt) | b4555 → | hypothetical protein |
| RA | 4,008,469 | +G | intergenic (+36/‑197) | b4555 → / → yigM | hypothetical protein/hypothetical protein |
| RA | 4,008,473 | +G | intergenic (+40/‑193) | b4555 → / → yigM | hypothetical protein/hypothetical protein |
| RA | 4,008,491 | 2 bp→CG | intergenic (+58/‑174) | b4555 → / → yigM | hypothetical protein/hypothetical protein |
| RA | 4,008,525 | +G | intergenic (+92/‑141) | b4555 → / → yigM | hypothetical protein/hypothetical protein |
| RA | 4,013,176 | C→G | G182R (GGA→CGA) | ysgA ← | hypothetical protein |
| RA | 4,013,177 | +C | coding (543/999 nt) | ysgA ← | hypothetical protein |
| RA | 4,013,717 | +G | coding (3/999 nt) | ysgA ← | hypothetical protein |
| RA | 4,013,772 | +C | intergenic (‑53/‑246) | ysgA ← / → udp | hypothetical protein/uridine phosphorylase |
| RA | 4,016,743 | C→T | P101L (CCC→CTC) | ubiE → | UbiE |
| RA | 4,019,857 | C→T | intergenic (+56/‑28) | b3836 → / → b3838 | hypothetical protein/hypothetical protein |
| RA | 4,019,860 | Δ2 bp | intergenic (+59/‑24) | b3836 → / → b3838 | hypothetical protein/hypothetical protein |
| RA | 4,021,684 | Δ1 bp | coding (542/609 nt)|coding (1/243 nt) | b4556 → tatD → |
hypothetical protein Mg‑dependent DNase |
| RA | 4,026,252 | 2 bp→GC | coding (110‑111/1164 nt) | fadA ← | thiolase I |
| RA | 4,031,984 | +C | coding (1250/1299 nt) | trkH → | TrkH |
| RA | 4,039,960 | Δ1 bp | intergenic (+42/‑36) | yihD → / → yihE | hypothetical protein/hypothetical protein |
| RA | 4,041,654 | G→A | intergenic (+29/‑125) | dsbA → / → b3861 | protein disulfide isomerase I/putative GTP‑binding protein |
| RA | 4,041,671 | (T)6→7 | intergenic (+46/‑108) | dsbA → / → b3861 | protein disulfide isomerase I/putative GTP‑binding protein |
| RA | 4,051,144 | Δ1 bp | intergenic (+146/+305) | hemN → / ← glnG | O2‑independent coproporphyrinogen III oxidase/GlnG |
| RA | 4,051,170 | +C | intergenic (+172/+279) | hemN → / ← glnG | O2‑independent coproporphyrinogen III oxidase/GlnG |
| RA | 4,055,398 | A→G | S73P (TCC→CCC) | glnA ← | glutamine synthetase |
| RA | 4,057,759 | +C | coding (1773/1776 nt) | yihK → | putative GTP‑binding factor |
| RA | 4,061,961 | Δ1 bp | coding (1386/1458 nt) | b3876 ← | putative permease |
| RA | 4,085,675 | Δ1 bp | intergenic (+38/+13) | yiiG → / ← frvR | hypothetical protein/putative frv operon regulatory protein |
| RA | 4,091,351 | C→T | G168D (GGC→GAC) | rhaD ← | rhamnulose‑phosphate aldolase |
| MC JC | 4,091,572 | 3461 bp→29 bp | [rhaD]–rhaB | [rhaD], rhaA, rhaB | |
| RA | 4,103,519 | +T | intergenic (‑268/‑530) | cpxR ← / → yiiP | transcriptional regulator in 2‑component system/putative transport system permease protein |
| RA | 4,131,917 | A→G | N168S (AAC→AGC) | katG → | catalase |
| RA | 4,133,368 | G→T | E652* (GAG→TAG) | katG → | catalase |
| RA | 4,139,669 | +C | coding (233/330 nt) coding (132/159 nt) |
yijI → b4558 ← |
hypothetical protein hypothetical protein |
| RA | 4,149,302 | T→C | Q459R (CAG→CGG) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,156,159 | A→G | T31A (ACG→GCG) | oxyR → | OxyR |
| RA | 4,158,827 | G→T | G61V (GGC→GTC) | yijC → | hypothetical protein |
| RA | 4,161,702 | C→G | A162G (GCA→GGA) | btuB → | BtuB |
| RA | 4,175,751 | T→G | F144V (TTC→GTC) | nusG → | NusG |
| RA | 4,175,949 | +G | intergenic (+82/‑76) | nusG → / → rplK | NusG/50S ribosomal subunit protein L11 |
| RA | 4,177,426 | T→C | intergenic (+265/‑148) | rplA → / → rplJ | 50S ribosomal subunit protein L1/50S ribosomal subunit protein L10 |
| RA | 4,184,644 | A→G | T573A (ACT→GCT) | rpoC → | RNA polymerase beta prime subunit |
| RA | 4,194,577 | 2 bp→GC | coding (97‑98/774 nt) | yjaD → | hypothetical protein |
| RA | 4,202,108 | A→G | E404G (GAA→GGA) | hydG → | HydG |
| RA | 4,216,491 | T→C | V106A (GTG→GCG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,229,642 | A→G | L391L (TTG→CTG) | lysC ← | aspartokinase III |
| RA | 4,273,643 | G→A | P198P (CCG→CCA) | yjcC → | hypothetical protein |
| RA | 4,277,306 | A→G | I417V (ATT→GTT) | yjcD → | hypothetical protein |
| RA | 4,293,960 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate‑aspartate symport protein/hypothetical protein |
| RA | 4,298,691 | A→G | V609A (GTC→GCC) | yjcQ ← | hypothetical protein |
| RA | 4,311,496 | +C | coding (301/408 nt) | phnQ ← | hypothetical protein |
| RA | 4,316,203 | T→A | Q47L (CAG→CTG) | phnK ← | ATP‑binding component of phosphonate transport |
| RA | 4,388,615 | A→G | V158A (GTG→GCG) | b4161 ← | hypothetical protein |
| RA | 4,429,526 | C→T | A12A (GCG→GCA) | ytfE ← | hypothetical protein |
| RA | 4,435,684 | +A | coding (400/501 nt) | ytfI → | hypothetical protein |
| RA | 4,448,541 | +C | intergenic (+46/‑92) | ytfQ → / → ytfR | putative LACI‑type transcriptional regulator/YtfR |
| RA | 4,448,543 | +C | intergenic (+48/‑90) | ytfQ → / → ytfR | putative LACI‑type transcriptional regulator/YtfR |
| RA | 4,449,738 | +G | coding (1106/1254 nt) | ytfR → | YtfR |
| RA | 4,472,408 | A→G | intergenic (+117/‑28) | b4251 → / → b4252 | hypothetical protein/hypothetical protein |
| RA | 4,474,826 | +A | intergenic (+1/+44) | yjgL → / ← argI | hypothetical protein/ornithine carbamoyltransferase 1 |
| MC JC | 4,474,849 | 20 bp→30 bp | intergenic (+24/+2) | yjgL → / ← argI | hypothetical protein/ornithine carbamoyltransferase 1 |
| RA | 4,477,041 | Δ1 bp | intergenic (‑151/‑269) | b4256 ← / → yjgN | hypothetical protein/hypothetical protein |
| RA | 4,477,068 | +C | intergenic (‑178/‑242) | b4256 ← / → yjgN | hypothetical protein/hypothetical protein |
| RA | 4,477,281 | Δ1 bp | intergenic (‑391/‑29) | b4256 ← / → yjgN | hypothetical protein/hypothetical protein |
| RA | 4,477,321 | Δ1 bp | coding (12/1182 nt) | yjgN → | hypothetical protein |
| RA | 4,478,503 | (A)7→6 | intergenic (+12/+47) | yjgN → / ← valS | hypothetical protein/valine tRNA synthetase |
| RA | 4,478,511 | Δ1 bp | intergenic (+20/+39) | yjgN → / ← valS | hypothetical protein/valine tRNA synthetase |
| RA | 4,478,527 | Δ1 bp | intergenic (+36/+23) | yjgN → / ← valS | hypothetical protein/valine tRNA synthetase |
| RA | 4,542,643 | Δ1 bp | intergenic (+46/‑22) | b4316 → / → fimD | Pil/FimD |
| RA | 4,544,170 | T→C | I502I (ATT→ATC) | fimD → | FimD |
| RA | 4,545,868 | A→G | K5K (AAA→AAG) | fimG → | FimG |
| RA | 4,558,365 | A→G | intergenic (‑104/‑134) | yjiH ← / → b4331 | hypothetical protein/hypothetical protein |
| RA | 4,573,190 | Δ1 bp | coding (1487/1542 nt) | yjiU → | hypothetical protein |
| RA | 4,576,170 | A→G | R246R (CGT→CGC) | mcrB ← | McrB |
| RA | 4,577,071 | A→G | *114Q (TAA→CAA) | yjiW ← | hypothetical protein |
| RA | 4,583,050 | G→A | Q446* (CAA→TAA) | hsdR ← | endonuclease R |
| RA | 4,588,821 | A→G | I15T (ATA→ACA) | yjiY ← | putative carbon starvation protein |
| RA | 4,593,254 | 2 bp→GC | coding (59‑60/807 nt) | yjjM ← | hypothetical protein |
| RA | 4,593,336 | +G | intergenic (‑23/‑208) | yjjM ← / → yjjN | hypothetical protein/putative oxidoreductase |
| RA | 4,600,078 | C→T | W135* (TGG→TAG) | yjjP ← | putative structural protein |
| RA | 4,603,664 | A→G | noncoding (71/88 nt) | leuV ← | tRNA‑Leu |
| RA | 4,608,595 | 2 bp→GC | intergenic (+23/‑369) | prfC → / → osmY | peptide chain release factor RF‑3/OsmY |
| RA | 4,614,238 | G→T | L133I (CTA→ATA) | yjjI ← | hypothetical protein |
| RA | 4,637,851 | C→T | V9I (GTT→ATT) | arcA ← | ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 363481 | 365527 | 2047 | 120 [119] | [117] 120 | lacZ | beta‑D‑galactosidase |
| * | * | ÷ | NC_000913 | 2518977–2519022 | 2519113–2519070 | 49–137 | 120 [119] | [119] 121 | [valU]–[valX] | [valU],[valX] |
| * | * | ÷ | NC_000913 | 3421324–3421870 | 3422239–3421880 | 11–916 | 122 [115] | [119] 121 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3943596–3943706 | 3943810–3943771 | 66–215 | 120 [116] | [114] 122 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 269765 = | NA (NA) | 229 (0.980) | 124/184 | 0.2 | 99.1% | coding (300/405 nt) | yi91a | hypothetical protein |
| ? | NC_000913 | = 370983 | 2 (0.010) | coding (536/882 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase | |||||
| * | ? | NC_000913 | = 279335 | NA (NA) | 238 (1.020) | 121/184 | 0.2 | 97.1% | coding (252/339 nt) | b4505 | hypothetical protein |
| ? | NC_000913 | 370982 = | 7 (0.030) | coding (535/882 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase | |||||
| * | ? | NC_000913 | = 483555 | 87 (0.400) | 131 (0.580) +CCC |
80/166 | 2.0 | 60.1% | coding (73/3150 nt) | acrB | acridine efflux pump |
| ? | NC_000913 | 483556 = | 87 (0.370) | coding (72/3150 nt) | acrB | acridine efflux pump | |||||
| * | ? | NC_000913 | = 1207028 | 131 (0.560) | 87 (0.450) | 65/152 | 2.9 | 48.2% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | NC_000913 | = 1208825 | 79 (0.410) | coding (57/540 nt) | b1157 | putative tail fiber protein | |||||
| * | ? | NC_000913 | 3192559 = | 224 (0.960) | 160 (0.860) +ATGTGTTAATGAAACCTTC |
77/146 | 1.3 | 46.9% | intergenic (+18/+402) | b3051/b3052 | putative membrane protein/putative kinase |
| ? | NC_000913 | = 3192916 | 233 (1.000) | intergenic (+375/+45) | b3051/b3052 | putative membrane protein/putative kinase | |||||
| * | ? | NC_000913 | 3349258 = | 20 (0.090) | 245 (1.050) | 119/184 | 0.3 | 92.5% | coding (1403/2331 nt) | arcB | aerobic respiration sensor‑response protein |
| ? | NC_000913 | = 3349263 | NA (NA) | coding (1398/2331 nt) | arcB | aerobic respiration sensor‑response protein | |||||