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 | 78,830 | T→A | 5.0% | intergenic (+31/+18) | setA → / ← leuD | broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit |
| RA | 107,554 | G→T | 16.6% | intergenic (+80/‑151) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 124,193 | A→G | 5.1% | K393E (AAA→GAA) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 216,066 | A→G | 5.3% | intergenic (+87/+113) | nlpE → / ← yaeF | lipoprotein involved with copper homeostasis and adhesion/putative lipoprotein |
| RA | 216,067 | A→C | 5.3% | intergenic (+88/+112) | nlpE → / ← yaeF | lipoprotein involved with copper homeostasis and adhesion/putative lipoprotein |
| RA | 216,073 | T→A | 5.3% | intergenic (+94/+106) | nlpE → / ← yaeF | lipoprotein involved with copper homeostasis and adhesion/putative lipoprotein |
| RA | 216,074 | T→A | 5.4% | intergenic (+95/+105) | nlpE → / ← yaeF | lipoprotein involved with copper homeostasis and adhesion/putative lipoprotein |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 292,302 | C→G | 7.2% | intergenic (+71/+20) | yagJ → / ← yagK | CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 303,615 | T→C | 7.4% | intergenic (+10/+238) | yagU → / ← ykgJ | DUF1440 family inner membrane acid resistance protein/UPF0153 cysteine cluster protein |
| RA | 354,608 | G→A | 8.5% | intergenic (+16/‑314) | prpE → / → codB | propionate‑‑CoA ligase/cytosine transporter |
| RA | 354,609 | T→C | 8.8% | intergenic (+17/‑313) | prpE → / → codB | propionate‑‑CoA ligase/cytosine transporter |
| RA | 354,616 | G→A | 9.1% | intergenic (+24/‑306) | prpE → / → codB | propionate‑‑CoA ligase/cytosine transporter |
| RA | 354,617 | T→C | 9.4% | intergenic (+25/‑305) | prpE → / → codB | propionate‑‑CoA ligase/cytosine transporter |
| RA | 357,775 | A→T | 6.4% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 357,778 | C→T | 5.0% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 380,105 | A→C | 7.3% | G246G (GGT→GGG) | yaiO ← | outer membrane protein |
| RA | 429,862 | G→A | 5.2% | E120K (GAA→AAA) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 556,412 | C→A | 7.3% | G48C (GGC→TGC) | ybcI ← | DUF457 family inner membrane protein |
| RA | 619,410 | T→C | 5.5% | T264A (ACG→GCG) | fepC ← | ferrienterobactin ABC transporter ATPase |
| RA | 721,734 | A→G | 6.6% | M894T (ATG→ACG) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 777,208 | A→C | 9.0% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 781,238 | T→A | 5.9% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 9.5% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 892,455 | G→C | 10.1% | V163V (GTG→GTC) | rimK → | ribosomal protein S6 modification protein |
| RA | 892,457 | T→A | 10.5% | I164N (ATT→AAT) | rimK → | ribosomal protein S6 modification protein |
| RA | 892,459 | G→C | 10.4% | D165H (GAC→CAC) | rimK → | ribosomal protein S6 modification protein |
| RA | 938,092 | T→G | 6.2% | H33Q (CAT→CAG) | rarA → | recombination intermediate processing DNA‑dependent ATPase |
| RA | 940,751 | T→C | 8.1% | intergenic (+31/‑208) | serS → / → dmsA | seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 940,754 | G→A | 8.3% | intergenic (+34/‑205) | serS → / → dmsA | seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 1,029,267 | C→T | 9.6% | A235T (GCC→ACC) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,092,170 | T→C | 6.2% | A40A (GCA→GCG) | pgaA ← | biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein |
| RA | 1,215,685 | A→G | 5.3% | intergenic (‑210/‑104) | bluF ← / → ycgZ | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein/RcsB connector protein for regulation of biofilm and acid‑resistance |
| RA | 1,226,114 | C→G | 6.2% | intergenic (‑34/‑486) | minC ← / → ycgJ | inhibitor of FtsZ ring polymerization/uncharacterized protein |
| RA | 1,226,115 | A→C | 8.0% | intergenic (‑35/‑485) | minC ← / → ycgJ | inhibitor of FtsZ ring polymerization/uncharacterized protein |
| RA | 1,226,119 | C→G | 5.6% | intergenic (‑39/‑481) | minC ← / → ycgJ | inhibitor of FtsZ ring polymerization/uncharacterized protein |
| RA | 1,287,187 | A→T | 6.5% | noncoding (50/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| RA | 1,351,228 | G→C | 14.0% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,466,201 | T→C | 6.6% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 5.1% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 6.8% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,500,679 | T→C | 5.3% | V36A (GTC→GCC) | tehA → | potassium‑tellurite ethidium and proflavin transporter |
| RA | 1,567,467 | G→T | 5.7% | intergenic (‑327/+37) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,580,217 | C→A | 6.2% | G192W (GGG→TGG) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,592,187 | G→T | 5.6% | L86M (CTG→ATG) | hipB ← | antitoxin of HipAB toxin‑antitoxin system |
| RA | 1,613,276 | G→T | 6.5% | intergenic (‑25/+39) | glsB ← / ← sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,613,277 | A→T | 6.9% | intergenic (‑26/+38) | glsB ← / ← sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,613,278 | A→T | 6.9% | intergenic (‑27/+37) | glsB ← / ← sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,613,279 | A→C | 6.9% | intergenic (‑28/+36) | glsB ← / ← sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,701,024 | A→T | 5.0% | D23V (GAC→GTC) | malY → | PLP‑dependent beta‑cystathionase and maltose regulon regulator |
| RA | 1,708,709 | T→A | 9.2% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 5.5% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 10.9% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 7.1% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,715,919 | T→G | 5.8% | intergenic (‑30/+29) | pdxY ← / ← tyrS | pyridoxamine kinase/tyrosyl‑tRNA synthetase |
| RA | 1,792,242 | T→A | 8.1% | intergenic (‑222/+25) | ydiV ← / ← nlpC | anti‑FlhD4C2 factor, inactive EAL family phosphodiesterase/putative C40 clan peptidase lipoprotein |
| RA | 1,901,959 | G→T | 5.3% | intergenic (‑374/‑89) | yoaE ← / → manX | putative membrane protein/conserved protein/fused mannose‑specific PTS enzymes: IIA component/IIB component |
| RA | 1,919,611 | C→T | 5.4% | P701L (CCG→CTG) | yebT → | MCE domain protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,985,112 | C→G | 5.9% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,091,575 | G→A | 7.4% | C160Y (TGC→TAC) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| RA | 2,145,781 | G→A | 7.8% | R839Q (CGG→CAG) | yegE → | putative diguanylate cyclase |
| RA | 2,153,498 | C→A | 5.5% | intergenic (+47/‑146) | sibA → / → sibB | sRNA antisense regulator of toxic IbsA protein/sRNA antisense regulator of toxic IbsB protein |
| RA | 2,153,501 | A→C | 5.1% | intergenic (+50/‑143) | sibA → / → sibB | sRNA antisense regulator of toxic IbsA protein/sRNA antisense regulator of toxic IbsB protein |
| RA | 2,153,503 | T→A | 6.0% | intergenic (+52/‑141) | sibA → / → sibB | sRNA antisense regulator of toxic IbsA protein/sRNA antisense regulator of toxic IbsB protein |
| RA | 2,169,664 | A→T | 7.1% | intergenic (+53/+29) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,665 | A→T | 7.2% | intergenic (+54/+28) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,671 | T→G | 6.5% | intergenic (+60/+22) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,169,672 | T→C | 7.2% | intergenic (+61/+21) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,177,234 | C→A | 13.0% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,304,649 | C→T | 5.2% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 5.4% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,319,581 | A→G | 5.6% | V99A (GTG→GCG) ‡ | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,319,582 | C→G | 5.6% | V99L (GTG→CTG) ‡ | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,319,585 | C→G | 5.7% | D98H (GAT→CAT) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,319,586 | C→T | 5.7% | A97A (GCG→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,358,643 | G→A | 6.4% | A68V (GCC→GTC) | rhmA ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,460,555 | A→T | 8.2% | intergenic (‑86/+95) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,462,677 | A→T | 5.6% | intergenic (+31/‑335) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,678 | T→A | 5.4% | intergenic (+32/‑334) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,679 | A→T | 5.8% | intergenic (+33/‑333) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,470,427 | C→A | 18.4% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,436 | C→A | 11.9% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,538,698 | G→A | 5.3% | H296Y (CAT→TAT) | cysM ← | cysteine synthase B (O‑acetylserine sulfhydrolase B) |
| RA | 2,662,468 | A→G | 7.6% | intergenic (‑337/+115) | iscR ← / ← trmJ | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,668,982 | T→C | 6.0% | intergenic (‑86/‑50) | hcaR ← / → hcaE | hca operon transcriptional regulator/3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,766,414 | G→A | 5.3% | R166Q (CGA→CAA) | rnlA → | CP4‑57 prophage; RNase LS |
| RA | 2,788,671 | A→T | 7.5% | intergenic (+22/‑314) | ygaQ → / → csiD | uncharacterized protein; putative enzyme/carbon starvation protein |
| RA | 2,788,673 | A→T | 8.3% | intergenic (+24/‑312) | ygaQ → / → csiD | uncharacterized protein; putative enzyme/carbon starvation protein |
| RA | 2,788,674 | A→T | 8.3% | intergenic (+25/‑311) | ygaQ → / → csiD | uncharacterized protein; putative enzyme/carbon starvation protein |
| RA | 2,788,676 | A→T | 8.0% | intergenic (+27/‑309) | ygaQ → / → csiD | uncharacterized protein; putative enzyme/carbon starvation protein |
| RA | 2,796,375 | T→A | 6.2% | I138F (ATT→TTT) | ygaU ← | uncharacterized protein |
| RA | 2,817,774 | A→T | 6.2% | intergenic (‑271/+10) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,822,841 | A→G | 5.6% | L310P (CTG→CCG) | recA ← | DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 3,020,510 | G→T | 5.7% | intergenic (+21/‑30) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,511 | C→G | 5.7% | intergenic (+22/‑29) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,020,512 | A→C | 5.7% | intergenic (+23/‑28) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,256,230 | G→A | 5.8% | A141V (GCG→GTG) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,270,082 | A→C | 7.8% | intergenic (+480/+134) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,324,952 | A→G | 9.2% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 9.3% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,956 | C→T | 9.1% | intergenic (‑45/+45) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,959 | C→T | 9.0% | intergenic (‑48/+42) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,334,704 | G→C | 5.1% | intergenic (+23/‑205) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,705 | C→T | 5.1% | intergenic (+24/‑204) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,423,396 | T→G | 5.4% | intergenic (+202/+27) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,531 | T→G | 5.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,613,961 | G→T | 7.9% | E99* (GAA→TAA) ‡ | nikA → | nickel/heme ABC transporter periplasmic binding protein |
| RA | 3,613,962 | A→C | 7.6% | E99A (GAA→GCA) ‡ | nikA → | nickel/heme ABC transporter periplasmic binding protein |
| RA | 3,642,358 | T→A | 5.5% | intergenic (+27/+22) | dtpB → / ← rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,642,361 | T→A | 5.6% | intergenic (+30/+19) | dtpB → / ← rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,708,427 | G→A | 5.8% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,428 | T→A | 5.3% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,708,429 | T→C | 5.8% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,811,219 | A→G | 5.1% | intergenic (‑67/+31) | mutM ← / ← rpmG | formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase/50S ribosomal subunit protein L33 |
| RA | 3,828,980 | A→C | 9.9% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,959,480 | A→T | 7.2% | intergenic (+35/+52) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,481 | C→G | 7.3% | intergenic (+36/+51) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 7.8% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,080,616 | C→A | 8.8% | G205C (GGC→TGC) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,080,621 | T→G | 9.4% | Q203P (CAA→CCA) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,094,415 | T→G | 5.2% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,171,648 | A→C | 5.7% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,171,753 | G→A | 5.8% | noncoding (117/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,189,448 | C→T | 33.3% | Q1367* (CAG→TAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 28.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,332,868 | G→T | 5.1% | R135R (CGC→CGA) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| RA | 4,362,578 | G→T | 66.9% | noncoding (49/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,559,337 | A→C | 11.9% | F64V (TTT→GTT) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,577,333 | C→A | 6.6% | C209F (TGC→TTC) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC |
| RA | 4,614,378 | A→G | 10.1% | intergenic (+118/+302) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 772981 | 774212 | 1232 | 69 [65] | [63] 66 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037679 | 1039319 | 1641 | 69 [64] | [64] 66 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 1166023 | 1167432 | 1410 | 66 [65] | [65] 66 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423742–3424234 | 3424583–3424238 | 5–842 | 71 [65] | [64] 66 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4427 | 134 (0.820) | 8 (0.050) | 3/264 | NT | 6.0% | coding (694/1287 nt) | thrC | L‑threonine synthase |
| ? | NC_000913 | = 4443 | 122 (0.790) | coding (710/1287 nt) | thrC | L‑threonine synthase | |||||
| * | ? | NC_000913 | 781369 = | 145 (0.890) | 27 (0.170) +GAAG |
10/270 | NT | 18.4% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 102 (0.630) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 1207790 = | 132 (0.810) | 83 (0.580) | 35/246 | NT | 43.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 100 (0.690) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 120 (0.740) | 57 (0.400) | 24/246 | NT | 35.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 100 (0.690) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 107 (0.680) | 55/270 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2817942 | 103 (0.630) | 9 (0.060) | 5/238 | NT | 8.2% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 114 (0.820) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 4094350 | 188 (1.150) | 12 (0.100) | 9/196 | NT | 9.6% | noncoding (35/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 4094719 = | 95 (0.830) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||