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 | 71,272 | G→T | 17.8% | A232A (GCC→GCA) | thiB ← | thiamine‑, thiamine pyrophosphate‑, thiamine monophosphate‑binding ABC transporter periplasmic protein; ThiBPQ thiamine, thiamine pyrophosphate importer |
| RA | 93,623 | C→A | 6.2% | T17N (ACC→AAC) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine:D‑glutamate ligase |
| JC | 101,845 | Δ3 bp | 8.6% | coding (54‑56/1152 nt) | ftsZ → | GTP‑binding tubulin‑like cell division protein |
| RA | 108,141 | G→A | 12.4% | Q65* (CAG→TAG) | yacG ← | DNA gyrase inhibitor |
| RA | 123,694 | G→T | 15.4% | G505C (GGT→TGT) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 148,663 | G→A | 9.9% | A19V (GCC→GTC) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 157,254 | C→A | 6.0% | intergenic (‑163/+15) | dksA ← / ← sfsA | transcriptional regulator of rRNA transcription, DnaK suppressor protein/sugar fermentation stimulation protein A |
| RA | 158,095 | C→A | 8.4% | G142C (GGT→TGT) | ligT ← | 2'‑5' RNA ligase |
| RA | 170,808 | G→A | 6.5% | R188C (CGC→TGC) | hemL ← | glutamate‑1‑semialdehyde aminotransferase (aminomutase) |
| RA | 241,185 | G→T | 9.7% | P124P (CCG→CCT) | yafJ → | putative amidotransfease |
| RA | 263,261 | G→C | 6.1% | G152G (GGC→GGG) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,270 | C→A | 5.6% | V149V (GTG→GTT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,285 | G→A | 5.2% | D144D (GAC→GAT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 274,938 | T→A | 11.9% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 302,432 | C→T | 5.5% | A33T (GCA→ACA) | ecpD ← | polymerized tip adhesin of ECP fibers |
| RA | 320,638 | C→T | 5.8% | T146T (ACG→ACA) | ykgH ← | putative inner membrane protein |
| RA | 325,307 | G→T | 6.2% | R45L (CGC→CTC) | betT → | choline transporter of high affinity |
| RA | 335,730 | A→G | 5.0% | intergenic (+276/‑146) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 339,232 | C→T | 5.6% | A213V (GCG→GTG) | yahK → | aldehyde reductase, NADPH‑dependent, Zn‑containing, broad specificity |
| RA | 349,643 | G→T | 23.8% | L409L (CTG→CTT) | prpE → | propionate‑‑CoA ligase |
| RA | 370,501 | G→A | 8.2% | intergenic (+164/‑414) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,524 | T→G | 9.3% | intergenic (+187/‑391) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,527 | C→T | 9.1% | intergenic (+190/‑388) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 392,189 | G→A | 6.2% | G32D (GGT→GAT) | sbmA → | microcin B17 transporter |
| RA | 425,406 | C→T | 11.1% | A149V (GCG→GTG) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 459,946 | C→T | 8.9% | A30V (GCC→GTC) | fadM → | long‑chain acyl‑CoA thioesterase III |
| RA | 469,361 | Δ1 bp | 7.8% | coding (940/1287 nt) | amtB → | ammonium transporter |
| RA | 485,431 | C→A | 7.1% | intergenic (+77/+135) | mscK → / ← ybaM | mechanosensitive channel protein, intermediate conductance, K+ regulated/DUF2496 family protein |
| RA | 515,928 | G→A | 5.7% | W19* (TGG→TGA) | ybbP → | putative ABC transporter permease |
| RA | 546,431 | G→T | 7.4% | V179V (GTG→GTT) | ybcF → | putative carbonate kinase |
| RA | 552,654 | C→T | 5.5% | A182T (GCA→ACA) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 574,569 | G→A | 9.3% | intergenic (‑220/+71) | borD ← / ← ybcV | DLP12 prophage; putative lipoprotein/DLP12 prophage; uncharacterized protein |
| RA | 577,301 | T→C | 6.8% | pseudogene (186/438 nt) | tfaD → | pseudogene, DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related |
| RA | 612,363 | G→T | 6.1% | L917F (TTG→TTT) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 645,627 | G→A | 6.5% | T107I (ACC→ATC) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 697,304 | C→T | 7.8% | E302K (GAG→AAG) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 707,683 | C→A | 8.7% | P192P (CCG→CCT) | ybfF ← | acyl‑CoA esterase |
| RA | 726,319 | G→C | 5.4% | A427A (GCG→GCC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,369 | A→G | 5.4% | A777A (GCA→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,375 | A→G | 6.4% | G779G (GGA→GGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,212 | G→A | 9.8% | R1058R (AGG→AGA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,479 | C→G | 5.6% | pseudogene (891/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 732,499 | T→C | 6.3% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 749,689 | G→A | 5.2% | T79I (ACC→ATC) | gltA ← | citrate synthase |
| RA | 776,600:1 | +T | 14.0% | intergenic (+1/‑3) | valZ → / → lysY | tRNA‑Val/tRNA‑Lys |
| RA | 797,038 | G→T | 6.9% | R275L (CGC→CTC) | ybhH → | putative PrpF family isomerase |
| RA | 808,322 | G→A | 6.3% | P199P (CCG→CCA) | bioD → | dethiobiotin synthetase |
| RA | 830,550 | Δ1 bp | 10.5% | coding (2025/2151 nt) | dinG → | ATP‑dependent DNA helicase |
| RA | 859,249:1 | +C | 8.7% | coding (152/663 nt) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 859,251 | G→T | 8.6% | G52C (GGT→TGT) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 866,850 | C→T | 5.2% | P143L (CCG→CTG) | gsiC → | glutathione transporter, permease component, ABC superfamily |
| RA | 895,178 | C→A | 6.5% | intergenic (+77/+122) | rlmC → / ← artJ | 23S rRNA m(5)U747 methyltransferase, SAM‑dependent/arginine binding protein, periplasmic |
| RA | 910,659 | G→A | 9.2% | intergenic (‑346/+149) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 968,114 | C→T | 6.7% | W248* (TGG→TGA) | ycbC ← | DUF218 superfamily protein |
| RA | 1,045,283 | T→G | 11.0% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,067,977 | C→A | 11.8% | D115Y (GAT→TAT) | rutB ← | ureidoacrylate amidohydrolase |
| RA | 1,108,540 | G→A | 9.6% | R741H (CGC→CAC) | opgH → | membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,186,948 | C→T | 9.9% | P165P (CCG→CCA) | purB ← | adenylosuccinate lyase |
| RA | 1,218,996 | G→A | 7.3% | intergenic (+91/‑24) | ymgJ → / → ycgI | uncharacterized protein/pseudogene |
| RA | 1,219,001 | T→A | 7.4% | intergenic (+96/‑19) | ymgJ → / → ycgI | uncharacterized protein/pseudogene |
| RA | 1,253,355 | G→A | 6.7% | intergenic (‑87/+30) | ychF ← / ← pth | catalase inhibitor protein; ATPase, K+‑dependent, ribosome‑associated/peptidyl‑tRNA hydrolase |
| RA | 1,278,892 | C→A | 8.3% | I1191I (ATC→ATA) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,282,322 | A→G | 5.2% | intergenic (+340/+200) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,421 | A→G | 10.3% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,430 | C→T | 10.4% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,439 | A→G | 11.5% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,322,638 | C→A | 7.4% | P244P (CCG→CCT) | yciK ← | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase |
| RA | 1,420,599 | C→A | 7.7% | intergenic (+260/‑112) | ydaY → / → tmpR | pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein |
| RA | 1,422,040 | A→G | 7.5% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,060 | G→C | 11.4% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,252 | A→G | 8.9% | pseudogene (732/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,309 | T→C | 6.4% | pseudogene (675/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 8.4% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,461,046 | C→T | 18.9% | pseudogene (1398/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,461,055 | A→G | 19.9% | pseudogene (1407/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,470,198 | C→A | 22.2% | D266E (GAC→GAA) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
| RA | 1,508,515 | G→A | 8.1% | W143* (TGG→TAG) | ydcU → | putative spermidine/putrescine transporter subunit |
| RA | 1,508,959 | T→C | 7.3% | L291P (CTG→CCG) | ydcU → | putative spermidine/putrescine transporter subunit |
| RA | 1,513,814 | G→A | 7.5% | V177V (GTG→GTA) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,528,856 | G→A | 14.8% | A192A (GCG→GCA) | nhoA → | N‑hydroxyarylamine O‑acetyltransferase |
| RA | 1,559,660 | T→C | 7.4% | S111G (AGC→GGC) | dosP ← | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| RA | 1,604,344 | A→C | 12.5% | I198M (ATT→ATG) | uxaB ← | altronate oxidoreductase, NAD‑dependent |
| RA | 1,610,132 | G→T | 14.3% | S38I (AGT→ATT) | yneK → | uncharacterized protein |
| RA | 1,623,848 | C→T | 14.0% | Q441Q (CAG→CAA) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,652,580 | C→A | 9.0% | S85R (AGC→AGA) | ynfE → | putative selenate reductase, periplasmic |
| RA | 1,681,729 | G→A | 18.0% | R302R (CGC→CGT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,732 | A→G | 18.0% | I301I (ATT→ATC) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,735 | C→A | 17.9% | V300V (GTG→GTT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,683,082 | C→T | 10.2% | L84L (CTG→TTG) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,700,087:1 | +C | 5.7% | coding (64/582 nt) | rsxA → | SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex |
| RA | 1,702,079 | G→A | 8.4% | E302K (GAA→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,767,150 | G→T | 7.3% | E128* (GAA→TAA) | ydiN → | MFS transporter superfamily protein |
| RA | 1,775,171 | C→A | 6.2% | P172T (CCG→ACG) | ydiR → | putative electron transfer flavoprotein, FAD‑binding subunit |
| RA | 1,864,310 | C→A | 7.9% | P367T (CCT→ACT) | yeaH → | UPF0229 family protein |
| RA | 1,900,847 | C→T | 7.6% | A157A (GCG→GCA) | rlmA ← | 23S rRNA m(1)G745 methyltransferase, SAM‑dependent |
| RA | 1,919,186 | A→G | 5.7% | I14T (ATC→ACC) | yobA ← | CopC family protein |
| RA | 1,933,273 | G→A | 9.0% | L456L (CTG→CTA) | pykA → | pyruvate kinase II |
| RA | 1,996,942 | G→T | 6.9% | A49E (GCG→GAG) | fliC ← | flagellar filament structural protein (flagellin) |
| RA | 2,011,900 | G→T | 9.5% | V12F (GTT→TTT) | fliK → | flagellar hook‑length control protein |
| RA | 2,055,734 | A→T | 8.9% | intergenic (‑320/‑7) | nac ← / → asnV | nitrogen assimilation regulon transcriptional regulator; autorepressor/tRNA‑Asn |
| RA | 2,057,140 | G→T | 6.3% | A270D (GCT→GAT) | cobT ← | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,059,656 | T→C | 10.3% | intergenic (‑21/+130) | yeeH ← / ← insH1 | pseudogene/IS5 transposase and trans‑activator |
| RA | 2,076,426 | G→A | 6.1% | V64I (GTA→ATA) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,139,091 | C→T | 8.3% | T782I (ACA→ATA) | yegE → | putative diguanylate cyclase |
| RA | 2,171,909 | G→A | 11.1% | R45R (CGC→CGT) | fbaB ← | fructose‑bisphosphate aldolase class I |
| RA | 2,245,164 | A→G | 22.2% | K282K (AAA→AAG) | nfo → | endonuclease IV with intrinsic 3'‑5' exonuclease activity |
| RA | 2,288,125 | C→T | 8.0% | A87T (GCT→ACT) | ccmF ← | heme lyase, CcmF subunit |
| RA | 2,335,147 | A→G | 6.0% | D834D (GAT→GAC) | yfaL ← | adhesin |
| RA | 2,335,151 | C→G | 6.1% | G833A (GGC→GCC) | yfaL ← | adhesin |
| RA | 2,369,417 | A→G | 6.7% | W9R (TGG→CGG) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,397,115 | C→T | 11.1% | L70L (CTG→CTA) | nuoC ← | NADH:ubiquinone oxidoreductase, fused CD subunit |
| RA | 2,412,229 | G→T | 6.9% | P143T (CCG→ACG) | yfcD ← | putative NUDIX hydrolase |
| RA | 2,430,734 | G→T | 5.8% | P199P (CCC→CCA) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,487,308 | G→A | 8.0% | L192L (CTG→TTG) | yfdX ← | uncharacterized protein |
| RA | 2,537,532 | C→A | 6.3% | G151C (GGC→TGC) | ucpA ← | furfural resistance protein, putative short‑chain oxidoreductase |
| RA | 2,549,264 | G→T | 6.7% | L166M (CTG→ATG) | eutL ← | putative ethanol utilization carboxysome structural protein |
| RA | 2,552,981 | G→A | 5.9% | W255* (TGG→TGA) | intZ → | CPZ‑55 prophage; putative phage integrase |
| RA | 2,597,713:1 | +C | 5.3% | coding (508/948 nt) | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,597,714 | A→G | 5.3% | N170S (AAT→AGT) ‡ | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,597,715 | T→A | 5.1% | N170K (AAT→AAA) ‡ | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,597,717 | C→T | 5.7% | T171M (ACG→ATG) | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,597,723 | C→T | 5.7% | A173V (GCG→GTG) | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,597,993 | C→A | 5.8% | S263* (TCA→TAA) | hyfC → | hydrogenase 4, membrane subunit |
| RA | 2,645,634 | G→A | 6.4% | R5C (CGC→TGC) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,675,209 | G→T | 8.2% | A299E (GCG→GAG) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,536 | G→T | 25.0% | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,748,318 | C→A | 8.7% | H22N (CAC→AAC) | smpB → | trans‑translation protein |
| RA | 2,754,345 | G→A | 11.6% | G147D (GGC→GAC) | yfjJ → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,805,396 | C→A | 15.9% | T204N (ACC→AAC) | emrA → | multidrug efflux system |
| RA | 2,886,451 | C→A | 8.4% | R146S (CGC→AGC) | ygcN → | putative oxidoreductase |
| RA | 2,905,169 | C→T | 14.8% | Q614Q (CAG→CAA) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,916,898 | G→T | 11.1% | I82I (ATC→ATA) | truC ← | tRNA(Ile1,Asp) pseudouridine(65) synthase |
| RA | 2,960,603 | C→T | 7.1% | P397P (CCG→CCA) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 2,966,898 | C→A | 8.9% | L108L (CTG→CTT) | lplT ← | lysophospholipid transporter |
| RA | 2,968,283 | G→T | 11.8% | P364Q (CCG→CAG) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 3,017,915 | G→T | 6.7% | G69V (GGT→GTT) | xanQ → | xanthine permease |
| RA | 3,048,677 | C→A | 12.5% | D43Y (GAC→TAC) | ygfB ← | UPF0149 family protein |
| RA | 3,062,410 | C→A | 12.1% | V253L (GTG→TTG) | mscS ← | mechanosensitive channel protein, small conductance |
| RA | 3,064,708 | G→C | 14.0% | intergenic (‑105/+110) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,064,718 | T→G | 25.0% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,103,785 | C→A | 14.7% | noncoding (61/76 nt) | pheV → | tRNA‑Phe |
| RA | 3,150,324 | C→A | 9.3% | H115N (CAT→AAT) | dkgA → | 2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,166,880 | C→T | 5.1% | A626T (GCG→ACG) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,171,284 | C→A | 7.7% | intergenic (‑15/‑190) | nudF ← / → tolC | ADP‑ribose pyrophosphatase/transport channel |
| RA | 3,202,082 | G→A | 5.6% | D234N (GAC→AAC) | ttdT → | L‑tartrate/succinate antiporte |
| RA | 3,203,023 | G→A | 10.5% | R294C (CGT→TGT) | tsaD ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein |
| RA | 3,203,041 | C→A | 5.8% | G288C (GGC→TGC) | tsaD ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein |
| RA | 3,275,868 | C→A | 7.0% | T178T (ACC→ACA) | agaS → | tagatose‑6‑phosphate ketose/aldose isomerase |
| RA | 3,300,764 | A→C | 5.6% | G152G (GGT→GGG) ‡ | deaD ← | ATP‑dependent RNA helicase |
| RA | 3,300,766 | C→T | 6.2% | G152S (GGT→AGT) ‡ | deaD ← | ATP‑dependent RNA helicase |
| RA | 3,303,762 | C→T | 10.2% | D256N (GAT→AAT) | pnp ← | polynucleotide phosphorylase/polyadenylase |
| RA | 3,416,501 | C→T | 9.1% | A236V (GCG→GTG) | yhdZ → | putative amino‑acid transporter subunit |
| RA | 3,416,890 | T→G | 19.4% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 19.2% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,502,647 | G→A | 7.3% | Q176* (CAG→TAG) | yhfW ← | phosphopentomutase‑related metalloenzyme superfamily protein |
| RA | 3,511,756 | C→A | 11.2% | P30P (CCG→CCT) | aroB ← | 3‑dehydroquinate synthase |
| RA | 3,532,457 | G→T | 6.3% | A572S (GCC→TCC) | yhgF → | putative transcriptional accessory protein |
| RA | 3,564,775 | C→T | 5.7% | T696T (ACG→ACA) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,597,253 | G→A | 7.4% | D117D (GAC→GAT) | ftsY ← | Signal Recognition Particle (SRP) receptor |
| RA | 3,618,613 | T→A | 7.4% | A292A (GCT→GCA) | yhhI → | putative transposase |
| RA | 3,690,535 | C→A | 9.9% | P240T (CCG→ACG) | bcsE → | cellulose production protein |
| RA | 3,695,065 | G→A | 5.5% | S381S (TCG→TCA) | yhjV → | putative transporter |
| RA | 3,732,233 | C→A | 6.2% | V459V (GTC→GTA) | malS → | alpha‑amylase |
| RA | 3,750,846 | G→T | 7.8% | G114G (GGC→GGA) | yiaY ← | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family |
| RA | 3,757,525 | T→C | 13.2% | L661L (CTT→CTC) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,764,145 | C→A | 9.6% | E199* (GAG→TAG) | yibH ← | putative membrane fusion protein (MFP) component of efflux pump |
| RA | 3,792,209 | G→T | 22.4% | S155* (TCA→TAA) | waaU ← | lipopolysaccharide core biosynthesis |
| RA | 3,871,524 | G→A | 7.5% | H652H (CAC→CAT) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,918,194 | C→A | 10.1% | G267V (GGG→GTG) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,973,351 | G→T | 9.8% | L12L (CTG→CTT) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,973,504 | C→A | 6.1% | N63K (AAC→AAA) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 3,982,420 | C→A | 6.2% | E3* (GAA→TAA) | hemX ← | putative uroporphyrinogen III methyltransferase |
| RA | 4,096,921 | G→A | 7.0% | W175* (TGG→TGA) | fieF → | ferrous iron and zinc transporter |
| RA | 4,097,962 | C→A | 6.0% | H161Q (CAC→CAA) | pfkA → | 6‑phosphofructokinase I |
| RA | 4,143,586 | C→T | 10.6% | intergenic (‑560/+38) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,154,053 | G→T | 5.8% | G163W (GGG→TGG) | btuB → | vitamin B12/cobalamin outer membrane transporter |
| RA | 4,165,450 | A→C | 13.4% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,167,038 | A→T | 7.7% | V389V (GTA→GTT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,167,041 | A→T | 7.6% | A390A (GCA→GCT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,178,500 | C→T | 62.5% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,208,305 | C→A | 9.6% | T423T (ACC→ACA) | aceA → | isocitrate lyase |
| RA | 4,252,148 | C→A | 8.9% | I184I (ATC→ATA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,274,144 | G→T | 14.0% | H229Q (CAC→CAA) | actP ← | acetate transporter |
| RA | 4,285,970 | C→T | 10.2% | intergenic (+248/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,196 | C→T | 9.3% | intergenic (+474/+57) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,315,681 | T→C | 5.4% | intergenic (‑123/+535) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,682 | A→G | 5.5% | intergenic (‑124/+534) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,315,782 | A→G | 10.0% | intergenic (‑224/+434) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,351,888 | C→A | 6.6% | intergenic (‑137/+120) | cadC ← / ← yjdQ | cadBA operon transcriptional activator/pseudogene, P4‑like integrase remnant |
| RA | 4,362,598 | G→T | 10.6% | intergenic (+110/‑28) | groL → / → yjeI | Cpn60 chaperonin GroEL, large subunit of GroESL/DUF4156 family lipoprotein |
| RA | 4,367,328 | C→A | 19.7% | G71V (GGC→GTC) | blc ← | outer membrane lipoprotein (lipocalin), cell division and growth function |
| RA | 4,408,853 | G→A | 7.0% | A197V (GCG→GTG) | ulaG ← | L‑ascorbate 6‑phosphate lactonase |
| RA | 4,498,906 | T→C | 5.7% | pseudogene (81/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,909 | G→T | 5.7% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,581 | G→A | 5.7% | V80I (GTT→ATT) pseudogene (44/504 nt) |
insA → insB1 → |
IS1 repressor TnpA IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,660 | T→G | 7.5% | pseudogene (123/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,684 | C→T | 5.4% | pseudogene (147/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,690 | T→G | 6.9% | pseudogene (153/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,699 | A→G | 7.3% | pseudogene (162/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,702 | T→C | 7.6% | pseudogene (165/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,897 | T→A | 7.9% | pseudogene (360/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,900 | C→T | 8.1% | pseudogene (363/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,903 | T→G | 7.5% | pseudogene (366/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,511,362 | C→A | 7.2% | G159V (GGC→GTC) | yjhF ← | putative transporter |
| RA | 4,539,712 | C→T | 6.0% | intergenic (+185/+58) | fimH → / ← gntP | minor component of type 1 fimbriae/fructuronate transporter |
| RA | 4,570,144 | G→T | 14.3% | A379D (GCC→GAC) | hsdS ← | specificity determinant for hsdM and hsdR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 578865 | 579149 | 285 | 7 [3] | [4] 5 | [appY] | [appY] |
| * | * | ÷ | CP009273 | 1635163 | 1635298 | 136 | 5 [3] | [3] 5 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| * | * | ÷ | CP009273 | 2462830 | 2463094 | 265 | 5 [4] | [4] 6 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463560 | 2463741 | 182 | 5 [4] | [2] 6 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2988772 | 2988948 | 177 | 5 [3] | [3] 5 | ygeN | pseudogene |
| * | * | ÷ | CP009273 | 3354183 | 3354337 | 155 | 5 [2] | [2] 6 | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein |
| * | * | ÷ | CP009273 | 3432042 | 3432495 | 454 | 8 [3] | [4] 5 | zntR | zntR |
| * | * | ÷ | CP009273 | 3745275 | 3745382 | 108 | 5 [4] | [3] 7 | [yiaU] | [yiaU] |
| * | * | ÷ | CP009273 | 3762969 | 3763224 | 256 | 5 [4] | [4] 7 | [yibV]–yibV | [yibV],yibV |
| * | * | ÷ | CP009273 | 3797643 | 3797741 | 99 | 8 [2] | [4] 5 | waaS | lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | CP009273 | 3798131 | 3798498 | 368 | 5 [4] | [3] 5 | [waaS] | [waaS] |
| * | * | ÷ | CP009273 | 4037430 | 4037548 | 119 | 6 [4] | [4] 5 | dsbA/yihF | periplasmic protein disulfide isomerase I/DUF945 family protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 32 (0.730) | 37 (0.840) | 17/248 | NT | 53.6% | 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 | 1203246 = | 16 (0.360) | 18 (0.470) | 11/216 | NT | 58.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 12 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 14 (0.320) | 26 (0.680) | 14/216 | NT | 68.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 12 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972854 = | 4 (0.090) | 37 (0.840) | 17/248 | NT | 90.2% | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 1972861 | 8 (0.180) | 48 (1.090) | 21/248 | NT | 85.7% | intergenic (‑407/‑373) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||