mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 4,613 | C→A | 7.2% | Q294K (CAG→AAG) | thrC → | L‑threonine synthase |
| RA | 35,227:4 | +G | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 35,227:5 | +T | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 35,227:6 | +A | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 35,227:7 | +G | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 35,227:8 | +T | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 35,227:10 | +A | 11.3% | coding (145/591 nt) | caiE ← | stimulator of CaiD and CaiB enzyme activities |
| RA | 89,348 | G→T | 8.4% | K483N (AAG→AAT) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3) |
| RA | 158,283 | G→T | 6.3% | A79D (GCC→GAC) | ligT ← | 2'‑5' RNA ligase |
| RA | 187,742 | C→T | 20.0% | R133R (CGC→CGT) | tsf → | translation elongation factor EF‑Ts |
| RA | 221,373:1 | +G | 11.7% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 11.9% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 12.2% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 12.2% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 12.5% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 12.5% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 12.5% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 12.8% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 12.5% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 13.1% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 13.5% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 14.1% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 17.8% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 17.9% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 19.7% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 235,769 | G→T | 12.8% | pseudogene (177/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 243,088 | C→A | 18.2% | intergenic (‑99/‑111) | dinJ ← / → yafL | antitoxin of YafQ‑DinJ toxin‑antitoxin system/putative lipoprotein and C40 family peptidase |
| RA | 252,656 | C→A | 7.3% | H65N (CAC→AAC) | gpt → | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase |
| RA | 262,559 | C→T | 5.0% | pseudogene (120/192 nt) | ykfK ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related |
| RA | 302,895 | G→T | 7.3% | L717I (CTC→ATC) | ecpC ← | ECP production outer membrane protein |
| RA | 330,901 | G→T | 5.5% | intergenic (‑168/‑90) | yahC ← / → yahD | putative inner membrane protein/ankyrin repeat protein |
| RA | 335,511 | A→G | 7.1% | intergenic (+57/‑365) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 353,286 | T→A | 8.5% | intergenic (+121/+216) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 353,289 | T→C | 8.9% | intergenic (+124/+213) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| JC JC | 370,378 | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences (–) +8 bp :: +ATCTGC | 16.2% | intergenic (+41/‑530) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,400 | G→A | 5.7% | intergenic (+63/‑515) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,428 | T→C | 8.7% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,430 | A→G | 7.4% | intergenic (+93/‑485) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,442 | T→C | 8.6% | intergenic (+105/‑473) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 431,498 | T→A | 6.9% | F137I (TTT→ATT) | thiL → | thiamine monophosphate kinase |
| RA | 517,301 | T→C | 7.3% | L477P (CTG→CCG) | ybbP → | putative ABC transporter permease |
| RA | 541,682 | C→T | 5.9% | A46A (GCG→GCA) | allD ← | ureidoglycolate dehydrogenase |
| RA | 561,445 | C→A | 7.6% | pseudogene (91/222 nt) | xisD ← | pseudogene, exisionase in defective prophage DLP12;Phage or Prophage Related |
| RA | 572,881 | G→A | 8.9% | G10S (GGT→AGT) | essD → | DLP12 prophage; putative phage lysis protein |
| RA | 633,718 | G→A | 5.9% | S104S (TCC→TCT) | dsbG ← | thiol:disulfide interchange protein, periplasmic |
| RA | 730,479 | C→G | 9.5% | pseudogene (891/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 733,913 | T→C | 8.3% | R122R (CGT→CGC) | ybfD → | H repeat‑associated putative transposase |
| RA | 733,915 | A→G | 8.4% | K123R (AAG→AGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 791,167 | C→A | 13.3% | A208D (GCC→GAC) | modA → | molybdate transporter subunit |
| RA | 798,822 | C→T | 10.5% | intergenic (+46/‑137) | ybhI → / → ybhJ | putative transporter/putative hydratase |
| RA | 802,072 | G→T | 5.1% | S222R (AGC→AGA) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 831,364 | C→T | 7.5% | R221W (CGG→TGG) | ybiB → | putative family 3 glycosyltransferase |
| RA | 843,451 | C→A | 8.5% | V4L (GTA→TTA) | glnH ← | glutamine transporter subunit |
| RA | 857,367 | C→A | 7.9% | A232A (GCG→GCT) | ybiW ← | putative pyruvate formate lyase |
| RA | 893,162 | C→A | 7.0% | S208* (TCG→TAG) | potI → | putrescine transporter subunit: membrane component of ABC superfamily |
| RA | 923,518 | G→A | 6.1% | G378G (GGC→GGT) | cydC ← | fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component |
| RA | 931,070 | G→A | 14.8% | P797P (CCG→CCA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 931,074 | G→C | 15.4% | A799P (GCG→CCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 931,084 | A→C | 15.5% | Q802P (CAG→CCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 934,753 | C→T | 6.6% | A435V (GCT→GTT) | rarA → | DNA‑dependent ATPase involved in processing recombination intermediates at replication forks |
| RA | 935,695 | C→A | 8.2% | A271D (GCC→GAC) | serS → | seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine |
| RA | 986,854 | T→C | 7.5% | N259N (AAT→AAC) | pepN → | aminopeptidase N |
| RA | 997,974 | G→A | 5.5% | A238T (GCT→ACT) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,049,974 | G→A | 9.9% | A554V (GCG→GTG) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,124,559 | C→T | 6.0% | A422V (GCT→GTT) | murJ → | putative peptidoglycan lipid II flippase |
| RA | 1,150,377 | G→A | 6.6% | A270A (GCG→GCA) | yceG → | septation protein, ampicillin sensitivity |
| RA | 1,162,039 | G→T | 6.3% | A167S (GCG→TCG) | ndh → | respiratory NADH dehydrogenase 2/cupric reductase |
| RA | 1,216,968 | G→T | 6.2% | pseudogene (1912/2648 nt) | ycgH → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,249,740 | C→A | 5.4% | A557S (GCT→TCT) | ycgV ← | putative adhesin |
| RA | 1,255,342 | C→A | 11.1% | T306T (ACG→ACT) | dauA ← | C4‑dicarboxylic acid transporter |
| RA | 1,282,249 | A→G | 8.2% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,608 | T→C | 5.9% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,386,783 | G→A | 10.3% | S179N (AGT→AAT) | pgrR → | murein peptide degradation regulator |
| RA | 1,422,060 | G→C | 10.5% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,132 | C→T | 6.6% | pseudogene (852/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,150 | C→T | 6.6% | pseudogene (834/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 5.9% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,435,752 | G→T | 5.8% | A83A (GCC→GCA) | hslJ ← | heat‑inducible lipoprotein involved in novobiocin resistance |
| RA | 1,460,567 | A→G | 7.5% | pseudogene (919/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,593 | C→G | 8.1% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,602 | T→C | 10.7% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 6.2% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,896 | C→T | 10.9% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,115 | T→C | 6.8% | pseudogene (1467/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,513,989 | C→T | 5.3% | P236S (CCG→TCG) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,522,243 | C→T | 5.2% | pseudogene (85/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,534,579 | G→A | 5.9% | Q757* (CAA→TAA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,537,305 | G→T | 11.8% | P338Q (CCG→CAG) | narU ← | nitrate/nitrite transporter |
| RA | 1,565,668 | G→A | 6.9% | T212I (ACC→ATC) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,583,241 | C→A | 10.3% | pseudogene (1096/1227 nt) | ydeT ← | pseudogene; putative outer membrane protein |
| RA | 1,593,036 | G→A | 9.1% | T477T (ACC→ACT) | lsrK ← | autoinducer‑2 (AI‑2) kinase |
| RA | 1,594,117 | G→A | 15.6% | A117V (GCA→GTA) | lsrK ← | autoinducer‑2 (AI‑2) kinase |
| RA | 1,629,745 | T→A | 7.2% | A120A (GCA→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,629,762 | T→C | 8.5% | T115A (ACT→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,673,066 | G→T | 10.0% | G128V (GGC→GTC) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,679,621 | C→T | 12.9% | V409M (GTG→ATG) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,784,034 | G→T | 8.5% | Q55H (CAG→CAT) | ydiE → | hemin uptake protein HemP homolog |
| RA | 1,785,755 | G→T | 9.3% | H175N (CAC→AAC) | ydiV ← | anti‑FlhD4C2 factor, inactive EAL family phosphodiesterase |
| RA | 1,912,600 | G→T | 7.4% | Q278H (CAG→CAT) | yebT → | MCE domain protein |
| RA | 1,928,790 | G→T | 5.1% | L24L (CTC→CTA) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 2,033,194 | C→T | 10.5% | T79M (ACG→ATG) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| RA | 2,109,742 | G→A | 9.3% | S289S (AGC→AGT) | wcaL ← | putative glycosyl transferase |
| RA | 2,217,814 | G→T | 6.2% | T179N (ACC→AAC) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,224,736 | A→G | 7.1% | Q80R (CAG→CGG) | yohK → | LrgB family inner membrane protein |
| RA | 2,298,492 | A→G | 6.8% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,337,310 | C→A | 12.5% | G113G (GGG→GGT) | yfaL ← | adhesin |
| RA | 2,341,366 | G→A | 5.1% | W168* (TGG→TGA) | nrdB → | ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| RA | 2,365,166 | C→T | 7.5% | Y260Y (TAC→TAT) | arnT → | 4‑amino‑4‑deoxy‑L‑arabinose transferase |
| RA | 2,367,106 | A→G | 8.0% | intergenic (‑89/+21) | pmrD ← / ← menE | inactive two‑component system connector protein/O‑succinylbenzoate‑CoA ligase |
| RA | 2,399,955 | C→A | 100% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,437,163 | A→G | 7.1% | M641V (ATG→GTG) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,437,724 | Δ1 bp | 7.4% | coding (507/549 nt) | epmC ← | Elongation Factor P Lys34 hydroxylase |
| RA | 2,481,148 | T→C | 7.7% | L1099P (CTA→CCA) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,499,919 | C→A | 6.0% | G65C (GGC→TGC) | ypdF ← | Xaa‑Pro aminopeptidase |
| RA | 2,518,005 | G→T | 5.7% | P78Q (CCG→CAG) | xapA ← | purine nucleoside phosphorylase II |
| RA | 2,535,092 | Δ1 bp | 9.1% | coding (780/834 nt) | cysU ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,535,093 | Δ1 bp | 9.1% | coding (779/834 nt) | cysU ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,535,094 | Δ1 bp | 9.1% | coding (778/834 nt) | cysU ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,537,033 | T→G | 5.4% | intergenic (‑146/+158) | cysP ← / ← ucpA | thiosulfate‑binding protein/furfural resistance protein, putative short‑chain oxidoreductase |
| RA | 2,550,583 | G→T | 8.2% | S25* (TCA→TAA) | eutC ← | ethanolamine ammonia‑lyase, small subunit (light chain) |
| RA | 2,607,874 | G→T | 6.3% | M194I (ATG→ATT) | focB → | putative formate transporter |
| RA | 2,677,576 | G→A | 5.5% | intergenic (+161/+37) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,678,532 | G→A | 18.2% | P112L (CCA→CTA) | glyA ← | serine hydroxymethyltransferase |
| RA | 2,703,152 | G→A | 10.5% | L74L (CTG→TTG) | rpoE ← | RNA polymerase sigma E factor |
| RA | 2,714,813 | G→T | 6.3% | W501L (TGG→TTG) | pka → | protein lysine acetyltransferase |
| RA | 2,719,536 | G→T | 24.3% | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,739,962 | C→T | 7.7% | R398H (CGT→CAT) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,762,984 | T→G | 7.5% | intergenic (+139/‑78) | yfjQ → / → yfjR | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,806,217 | G→T | 8.4% | L81L (CTG→CTT) | emrB → | multidrug efflux system protein |
| RA | 2,811,275 | T→G | 17.3% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,814,979 | G→A | 9.2% | T131I (ACC→ATC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,843,524 | G→A | 5.2% | R91W (CGG→TGG) | hycA ← | regulator of the transcriptional regulator FhlA |
| RA | 2,928,793 | C→A | 5.1% | V400V (GTC→GTA) | fucP → | L‑fucose transporter |
| RA | 2,929,562 | C→A | 11.9% | A207E (GCG→GAG) | fucI → | L‑fucose isomerase |
| RA | 3,037,040 | C→A | 6.3% | T7N (ACC→AAC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,040,197 | G→A | 6.2% | P735L (CCG→CTG) | gcvP ← | glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,063,116 | C→A | 5.6% | L17L (CTG→CTT) | mscS ← | mechanosensitive channel protein, small conductance |
| RA | 3,087,812 | G→A | 7.5% | L210L (CTG→TTG) | yggR ← | putative PilT family AAA+ ATPase |
| RA | 3,107,243 | C→A | 6.7% | V157L (GTA→TTA) | pppA ← | bifunctional prepilin leader peptidase/ methylase |
| RA | 3,128,961 | C→T | 7.0% | G257D (GGC→GAC) | pitB ← | phosphate transporter |
| RA | 3,267,478 | G→T | 5.0% | N263K (AAC→AAA) | garP ← | putative (D)‑galactarate transporter |
| RA | 3,416,810 | G→A | 7.4% | noncoding (92/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,890 | T→G | 10.5% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,448,174 | C→T | 5.6% | R195H (CGC→CAC) | gspA ← | general secretory pathway component, cryptic |
| RA | 3,464,590 | G→A | 5.3% | T33T (ACC→ACT) | tufA ← | translation elongation factor EF‑Tu 1 |
| RA | 3,493,486 | A→T | 6.7% | N73I (AAT→ATT) | frlA → | putative fructoselysine transporter |
| RA | 3,546,241 | G→T | 5.8% | intergenic (‑409/‑203) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,548,003 | G→A | 5.6% | Q520Q (CAG→CAA) | malT → | mal regulon transcriptional activator |
| RA | 3,590,467 | C→T | 5.1% | A152T (GCA→ACA) | livK ← | leucine transporter subunit |
| RA | 3,607,907 | C→A | 14.1% | A294E (GCG→GAG) | nikA → | nickel‑binding, heme‑binding periplasmic protein |
| RA | 3,608,854 | C→A | 5.1% | A85D (GCC→GAC) | nikB → | nickel transporter subunit |
| RA | 3,618,205 | A→T | 16.0% | P156P (CCA→CCT) | yhhI → | putative transposase |
| RA | 3,671,762 | G→T | 12.9% | intergenic (‑52/+18) | yhjG ← / ← yhjH | putative inner membrane‑anchored periplasmic AsmA family protein/cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| RA | 3,690,677 | G→A | 5.6% | R287H (CGT→CAT) | bcsE → | cellulose production protein |
| RA | 3,703,793 | A→G | 7.6% | L15L (TTG→CTG) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,707,152 | C→A | 10.6% | N47K (AAC→AAA) | yiaC → | putative acyl‑CoA transferase |
| RA | 3,711,059 | G→T | 7.2% | W130C (TGG→TGT) | ghrB → | glyoxylate/hydroxypyruvate reductase B |
| RA | 3,788,171 | C→T | 7.8% | F275F (TTC→TTT) | hldD → | ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| RA | 3,851,607 | G→T | 7.3% | T53K (ACG→AAG) | yidJ ← | sulfatase/phosphatase superfamily protein |
| RA | 3,869,526 | C→A | 6.1% | A263S (GCT→TCT) | yidA ← | sugar phosphate phosphatase; substrates include erythrose 4‑P and mannose 1‑P phosphatase |
| RA | 3,922,352 | T→C | 7.8% | E204E (GAA→GAG) | viaA ← | stimulator of RavA ATPase activity; von Willebrand factor domain protein |
| RA | 3,932,260 | G→A | 12.1% | G225E (GGG→GAG) | rbsR → | transcriptional repressor of ribose metabolism |
| RA | 3,936,724 | T→A | 8.7% | intergenic (+15/‑71) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 3,944,266 | G→A | 7.3% | pseudogene (347/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 4,001,021 | Δ1 bp | 6.1% | coding (1798/1830 nt) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,076,588 | T→C | 6.4% | P865P (CCA→CCG) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,143,375 | A→G | 6.1% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,165,449 | C→T | 18.7% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 17.1% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,886 | G→A | 11.7% | K5K (AAG→AAA) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,176,469 | A→G | 81.0% | K398E (AAG→GAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,210,112 | C→A | 8.6% | P530Q (CCG→CAG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,221,292 | G→A | 6.3% | R90C (CGC→TGC) | yjbD ← | DUF3811 family protein |
| RA | 4,228,029 | G→T | 7.9% | L156L (CTG→CTT) | yjbH → | DUF940 family extracellular polysaccharide protein |
| RA | 4,231,860 | C→T | 6.6% | G108D (GGT→GAT) | xylE ← | D‑xylose transporter |
| RA | 4,239,280 | G→A | 9.7% | intergenic (+41/‑202) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,336,205 | G→A | 7.3% | G313G (GGC→GGT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,366,743 | G→A | 10.0% | V18I (GTT→ATT) | sugE → | multidrug efflux system protein |
| RA | 4,370,464 | C→T | 5.7% | A558T (GCT→ACT) | frdA ← | fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit |
| RA | 4,375,030 | G→T | 6.4% | E459* (GAA→TAA) | yjeM → | putative transporter |
| RA | 4,376,463 | C→T | 8.5% | V909I (GTT→ATT) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,415,412 | C→A | 5.5% | H26N (CAC→AAC) | priB → | primosomal protein N |
| RA | 4,573,155 | C→A | 15.1% | pseudogene (3478/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| RA | 4,597,545 | C→T | 5.1% | intergenic (‑28/‑75) | rsmC ← / → holD | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent/DNA polymerase III, psi subunit |
| RA | 4,614,692 | A→T | 5.5% | intergenic (‑86/‑20) | ytjB ← / → serB | SMP_2 family putative membrane‑anchored periplasmic protein/3‑phosphoserine phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 578881 | 579074 | 194 | 7 [6] | [5] 7 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 1459352 | 1459482 | 131 | 10 [6] | [5] 8 | [ynbG] | [ynbG] |
| * | * | ÷ | CP009273 | 2027304 | 2027428 | 125 | 8 [6] | [6] 10 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2208334 | 2209051 | 718 | 7 [5] | [5] 7 | [mlrA] | [mlrA] |
| * | * | ÷ | CP009273 | 2462825 | 2463038 | 214 | 7 [4] | [6] 7 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2988477 | 2988711 | 235 | 7 [6] | [6] 11 | [ygeN] | [ygeN] |
| * | * | ÷ | CP009273 | 3792470 | 3792706 | 237 | 8 [6] | [5] 7 | [waaU]–[waaZ] | [waaU],[waaZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 37 (0.640) | 53 (0.910) | 25/248 | NT | 58.9% | 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 | 370386 = | NA (NA) | 24 (0.630) | 8/162 | NT | 32.7% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372978 = | 55 (1.310) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | = 603466 | 55 (0.950) | 8 (0.150) | 3/224 | NT | 10.3% | intergenic (+22/‑55) | hokE/insL1 | toxic polypeptide, small/IS186 transposase |
| ? | CP009273 | 604816 = | 89 (1.700) | intergenic (+183/+99) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | CP009273 | 1203246 = | 22 (0.380) | 16 (0.320) | 13/216 | NT | 51.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 11 (0.220) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 20 (0.350) | 18 (0.360) | 10/216 | NT | 55.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 11 (0.220) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||