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 | 164,581 | A→C | 21.4% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 164,595 | T→G | 17.8% | intergenic (+61/‑135) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 238,535 | G→T | 6.9% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 289,256 | G→C | 7.1% | intergenic (‑94/+45) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 289,257 | T→A | 7.2% | intergenic (‑95/+44) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 299,984 | T→G | 7.2% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 357,775 | A→T | 5.8% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 380,004 | A→C | 5.9% | intergenic (‑123/+65) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 454,873 | C→G | 7.6% | intergenic (+84/‑260) | bolA → / → tig | stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor) |
| RA | 475,971 | C→G | 5.2% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 5.2% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 708,020 | C→A | 9.2% | intergenic (+263/‑314) | glnS → / → chiP | glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars |
| RA | 710,170 | C→T | 5.2% | intergenic (+54/+30) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 710,173 | A→G | 5.1% | intergenic (+57/+27) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 756,150 | C→T | 100% | Q82* (CAG→TAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 777,208 | A→C | 9.7% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 781,238 | T→A | 5.1% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 5.9% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,269 | C→T | 5.3% | intergenic (+47/‑100) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,719 | A→T | 8.0% | intergenic (+67/‑366) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 915,215 | T→G | 6.2% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,151,888 | T→G | 5.6% | intergenic (+37/‑51) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,286,944 | T→G | 6.7% | intergenic (+418/+122) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,149 | G→A | 6.1% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,351,220 | T→A | 10.8% | intergenic (‑181/+187) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,351,228 | G→C | 9.6% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,466,336 | C→G | 6.0% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,495 | C→T | 5.9% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 6.3% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,630 | G→C | 6.7% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,639 | C→T | 6.9% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,708,709 | T→A | 6.1% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 5.0% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 8.3% | 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 | 7.2% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,720,364 | G→T | 8.2% | intergenic (+21/+26) | slyB → / ← slyA | outer membrane lipoprotein/global transcriptional regulator |
| RA | 1,792,241 | A→T | 5.1% | intergenic (‑221/+26) | ydiV ← / ← nlpC | anti‑FlhD4C2 factor, inactive EAL family phosphodiesterase/putative C40 clan peptidase lipoprotein |
| RA | 1,864,768 | T→C | 6.3% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,885,422 | A→T | 6.4% | E253V (GAA→GTA) | yeaW → | putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,985,112 | C→G | 5.0% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,090,122 | A→G | 5.7% | intergenic (+76/‑70) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,124 | C→G | 5.5% | intergenic (+78/‑68) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,126 | C→T | 5.7% | intergenic (+80/‑66) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| 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 | 14.5% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 15.8% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,279 | C→A | 6.3% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,229,177 | A→C | 14.5% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,229,322 | C→G | 5.4% | intergenic (+257/+116) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,229,323 | C→G | 5.4% | intergenic (+258/+115) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,247,032 | T→C | 5.1% | intergenic (‑263/+31) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,247,033 | T→C | 5.1% | intergenic (‑264/+30) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,304,649 | C→T | 14.1% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,680 | T→C | 7.5% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,798 | T→A | 5.0% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,383,959 | A→T | 5.0% | intergenic (+35/+36) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,464,224 | T→C | 5.1% | intergenic (+154/+28) | yfdF → / ← mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,464,225 | T→G | 5.3% | intergenic (+155/+27) | yfdF → / ← mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,464,226 | T→C | 5.1% | intergenic (+156/+26) | yfdF → / ← mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,464,228 | C→A | 5.2% | intergenic (+158/+24) | yfdF → / ← mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,470,427 | C→A | 18.7% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,436 | C→A | 13.1% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,521,344 | C→T | 6.0% | intergenic (+16/+249) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,521,346 | A→T | 5.6% | intergenic (+18/+247) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,521,348 | A→G | 6.4% | intergenic (+20/+245) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,533,415 | T→A | 5.3% | intergenic (+35/‑349) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,725,824 | C→A | 7.8% | intergenic (‑78/+245) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,800,515 | C→A | 5.8% | intergenic (+40/‑208) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,800,517 | T→A | 5.6% | intergenic (+42/‑206) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,800,519 | T→G | 5.7% | intergenic (+44/‑204) | ygaM → / → nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| RA | 2,817,916 | T→G | 6.7% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,900,322 | C→T | 5.6% | intergenic (‑49/‑270) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,900,324 | G→T | 5.7% | intergenic (‑51/‑268) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,900,327 | A→C | 5.8% | intergenic (‑54/‑265) | ygcW ← / → yqcE | putative SDR family oxidoreductase/putative MFS transporter, inner membrane protein |
| RA | 2,998,332 | T→A | 6.1% | pseudogene (497/1137 nt) | ygeQ ← | pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant |
| RA | 3,046,050 | T→G | 7.6% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,239,609 | T→G | 6.4% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,612 | A→C | 11.9% | intergenic (+67/‑332) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,263,518 | T→A | 9.5% | N48I (AAT→ATT) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,269,956 | T→C | 8.6% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,332,822 | G→A | 5.8% | intergenic (‑87/+40) | yhbE ← / ← rpmA | EamA family inner membrane putative transporter/50S ribosomal subunit protein L27 |
| RA | 3,332,823 | T→C | 5.9% | intergenic (‑88/+39) | yhbE ← / ← rpmA | EamA family inner membrane putative transporter/50S ribosomal subunit protein L27 |
| RA | 3,334,704 | G→C | 6.0% | intergenic (+23/‑205) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,334,705 | C→T | 5.4% | intergenic (+24/‑204) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,368,219 | G→A | 6.4% | T131T (ACG→ACA) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,220 | C→G | 6.3% | L132V (CTG→GTG) ‡ | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,221 | T→C | 6.5% | L132P (CTG→CCG) ‡ | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,439,588 | G→C | 5.9% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 5.9% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,458,110 | C→A | 100% | T578T (ACC→ACA) | gspD → | general secretory pathway component, cryptic |
| RA | 3,470,106 | C→T | 5.3% | intergenic (‑253/+39) | chiA ← / ← tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| RA | 3,470,107 | G→T | 5.1% | intergenic (‑254/+38) | chiA ← / ← tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| RA | 3,470,108 | A→C | 5.8% | intergenic (‑255/+37) | chiA ← / ← tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| RA | 3,470,109 | A→G | 5.5% | intergenic (‑256/+36) | chiA ← / ← tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| RA | 3,482,325 | G→A | 100% | R346H (CGC→CAC) | yheS → | ABC‑F family protein predicted regulatory ATPase |
| RA | 3,504,855 | T→G | 5.7% | intergenic (+72/+80) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,504,861 | T→A | 10.8% | intergenic (+78/+74) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,504,880 | A→C | 5.5% | intergenic (+97/+55) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,539,815 | A→T | 5.3% | intergenic (+109/‑348) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,816 | T→A | 5.0% | intergenic (+110/‑347) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,817 | A→T | 5.1% | intergenic (+111/‑346) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| 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 | 3,608,695 | C→G | 10.9% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,728,125 | T→G | 6.1% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,781,022 | T→G | 9.6% | intergenic (+5/‑193) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,067 | T→G | 11.8% | intergenic (+50/‑148) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,100 | G→C | 6.5% | intergenic (+83/‑115) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,158 | A→C | 6.7% | intergenic (+141/‑57) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,828,980 | A→C | 8.1% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,891,502 | C→G | 5.3% | intergenic (+19/‑113) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,891,504 | T→A | 5.4% | intergenic (+21/‑111) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,891,506 | C→G | 5.0% | intergenic (+23/‑109) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,908,514 | A→T | 10.2% | intergenic (‑148/+35) | pstB ← / ← pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| RA | 3,959,457 | T→G | 9.5% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,482 | A→C | 7.9% | intergenic (+37/+50) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 7.4% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,966,862 | G→A | 17.8% | R149H (CGT→CAT) | rho → | transcription termination factor |
| RA | 3,966,877 | C→A | 12.6% | T154N (ACT→AAT) | rho → | transcription termination factor |
| RA | 3,967,036 | T→A | 7.5% | L207Q (CTG→CAG) | rho → | transcription termination factor |
| RA | 3,967,449 | C→T | 43.9% | L345F (CTC→TTC) | rho → | transcription termination factor |
| RA | 3,998,056 | T→G | 6.0% | L25R (CTT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,041,216 | T→C | 5.1% | Q73R (CAG→CGG) ‡ | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,041,217 | G→A | 5.1% | Q73* (CAG→TAG) ‡ | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,041,220 | T→C | 5.1% | S72G (AGC→GGC) | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,051,259 | G→T | 5.5% | noncoding (224/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,051,262 | A→C | 5.0% | noncoding (227/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,060,261 | G→T | 6.0% | intergenic (+31/‑186) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,060,264 | A→C | 6.2% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,087,021 | C→A | 6.0% | S7Y (TCT→TAT) | yiiG → | DUF3829 family lipoprotein |
| RA | 4,094,415 | T→G | 5.0% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,153,447 | A→G | 5.0% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,616 | C→T | 5.4% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,171,872 | A→C | 5.5% | intergenic (+116/‑185) | rrfB → / → murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| RA | 4,296,060 | C→T | 29.5% | 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 | 4,366,854 | T→G | 7.3% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,366,855 | C→A | 6.3% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,473,927 | C→A | 100% | A43S (GCC→TCC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,612,329 | A→G | 5.2% | intergenic (+40/‑82) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| RA | 4,612,330 | G→C | 5.3% | intergenic (+41/‑81) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| RA | 4,612,331 | C→T | 5.5% | intergenic (+42/‑80) | ytjA → / → yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 448590 | 450707 | 2118 | 269 [246] | [244] 256 | [cyoC]–[cyoA] | [cyoC],cyoB,[cyoA] |
| * | * | ÷ | NC_000913 | 1166004 | 1167440 | 1437 | 253 [248] | [247] 253 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423707–3424234 | 3424584–3424238 | 5–878 | 253 [249] | [249] 252 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 16653 | NA (NA) | 3 (0.010) | 3/264 | NT | NA | noncoding (1267/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 16691 | NA (NA) | noncoding (1305/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 50327 = | NA (NA) | 8 (0.020) | 6/264 | NT | NA | noncoding (1/37 nt) | REP5 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP5 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 50360 = | NA (NA) | noncoding (34/37 nt) | REP5 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP5 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 138717 = | NA (NA) | 16 (0.040) | 4/264 | NT | NA | noncoding (19/98 nt) | RIP10 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP10 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 3639299 | NA (NA) | noncoding (91/98 nt) | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 274380 | NA (NA) | 4 (0.010) | 3/268 | NT | NA | noncoding (770/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274493 | NA (NA) | noncoding (657/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 381669 | NA (NA) | 7 (0.020) | 5/264 | NT | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 4 (0.010) | 3/260 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 430986 = | NA (NA) | 5 (0.010) | 4/264 | NT | NA | noncoding (19/98 nt) | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 3740971 = | NA (NA) | noncoding (8/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 543165 | NA (NA) | 9 (0.020) | 6/264 | NT | NA | noncoding (79/97 nt) | RIP50 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP50 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 543176 | NA (NA) | noncoding (90/97 nt) | RIP50 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP50 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 610135 = | NA (NA) | 8 (0.020) | 4/264 | NT | NA | noncoding (19/98 nt) | RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3563589 = | NA (NA) | noncoding (8/98 nt) | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 715282 = | NA (NA) | 6 (0.010) | 3/264 | NT | NA | noncoding (19/98 nt) | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3563589 = | NA (NA) | noncoding (8/98 nt) | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 781369 = | 333 (0.780) | 56 (0.130) +GAAG |
28/270 | NT | 16.5% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 251 (0.590) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 899775 | NA (NA) | 8 (0.020) | 4/264 | NT | NA | noncoding (80/98 nt) | RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP82 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3740971 = | NA (NA) | noncoding (8/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 937227 = | NA (NA) | 12 (0.030) | 8/262 | NT | NA | noncoding (4/36 nt) | REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP85 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 937261 = | NA (NA) | intergenic (+48/‑111) | ftsK/lolA | DNA translocase at septal ring sorting daughter chromsomes/lipoprotein chaperone | |||||
| * | ? | NC_000913 | 1207790 = | 226 (0.530) | 154 (0.410) | 90/246 | NT | 44.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 187 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 226 (0.530) | 195 (0.520) | 102/246 | NT | 50.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 187 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 355 (0.850) | 152/270 | 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 | 2066466 = | NA (NA) | 4 (0.010) | 3/268 | NT | NA | noncoding (888/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2101951 = | NA (NA) | noncoding (993/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2538614 | NA (NA) | 13 (0.030) | 5/264 | NT | NA | noncoding (80/98 nt) | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 2538625 | NA (NA) | noncoding (91/98 nt) | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 2714283 = | NA (NA) | 4 (0.010) | 3/264 | NT | NA | noncoding (1/98 nt) | RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2714308 = | NA (NA) | noncoding (26/98 nt) | RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP188 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 2817942 | 305 (0.710) | 26 (0.070) | 16/238 | NT | 8.3% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 314 (0.860) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 3255287 | NA (NA) | 5 (0.010) | 3/266 | NT | NA | noncoding (71/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 3255319 | NA (NA) | noncoding (103/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 3330539 | NA (NA) | 7 (0.020) | 5/264 | NT | NA | noncoding (80/98 nt) | RIP243 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP243 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3740971 = | NA (NA) | noncoding (8/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 3563582 = | NA (NA) | 4 (0.010) | 4/264 | NT | NA | noncoding (1/98 nt) | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3563607 = | NA (NA) | noncoding (26/98 nt) | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 3620350 | NA (NA) | 10 (0.020) | 5/266 | NT | 100% | coding (1159/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3620425 | 0 (0.000) | coding (1234/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3740964 = | NA (NA) | 11 (0.030) | 7/264 | NT | NA | noncoding (1/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3740989 = | NA (NA) | noncoding (26/98 nt) | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP269 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4295801 = | NA (NA) | 27 (0.070) +GTGTGAAT |
6/262 | NT | 5.4% | intergenic (+7/+635) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | 4296061 = | 506 (1.180) | noncoding (227/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4542682 = | 318 (0.740) | 54 (0.130) | 37/260 | NT | 15.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 307 (0.770) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 311 (0.730) | 56 (0.140) | 34/260 | NT | 15.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 307 (0.770) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||