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 | 18,243 | A→G | 10.5% | E252G (GAG→GGG) | nhaA → | sodium‑proton antiporter |
| RA | 37,255 | A→C | 18.1% | G190G (GGT→GGG) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 52,342 | A→C | 9.5% | V30G (GTG→GGG) | rsmA ← | 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM‑dependent |
| RA | 57,545 | T→G | 12.1% | V61G (GTG→GGG) | djlA → | membrane‑anchored DnaK co‑chaperone, DNA‑binding protein |
| RA | 173,223 | A→G | 9.3% | S588G (AGT→GGT) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 199,049 | T→G | 12.4% | G374G (GGT→GGG) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| RA | 230,100 | A→C | 8.8% | V261G (GTG→GGG) | yafC ← | LysR family putative transcriptional regulator |
| RA | 243,044 | T→C | 9.2% | E87G (GAG→GGG) | fadE ← | acyl coenzyme A dehydrogenase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 300,989 | A→G | 9.5% | L300P (CTC→CCC) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 334,255 | T→C | 9.9% | E60G (GAG→GGG) | yahB ← | putative DNA‑bindng transcriptional regulator |
| RA | 335,249 | G→A | 8.1% | intergenic (‑227/‑31) | yahC ← / → yahD | putative inner membrane protein/ankyrin repeat protein |
| RA | 380,139 | A→C | 11.7% | V235G (GTG→GGG) | yaiO ← | outer membrane protein |
| RA | 386,014 | T→G | 11.1% | G261G (GGT→GGG) | tauA → | taurine ABC transporter periplasmic binding protein |
| RA | 388,319 | C→G | 17.4% | R175R (CGC→CGG) | tauD → | taurine dioxygenase, 2‑oxoglutarate‑dependent |
| RA | 388,772 | T→C | 11.7% | E319G (GAG→GGG) | hemB ← | 5‑aminolevulinate dehydratase (porphobilinogen synthase) |
| RA | 429,830 | T→G | 14.1% | V109G (GTG→GGG) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 433,649 | T→G | 35.8% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 62.8% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 462,674 | A→G | 9.6% | S254G (AGC→GGC) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 511,938 | T→C | 10.1% | S100P (TCA→CCA) | glsA → | glutaminase 1 |
| RA | 540,546 | C→T | 10.1% | intergenic (+38/‑19) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 540,600 | A→T | 11.0% | L12F (TTA→TTT) | ybbY → | putative uracil/xanthine transporter |
| RA | 540,610 | C→T | 9.7% | Q16* (CAG→TAG) | ybbY → | putative uracil/xanthine transporter |
| RA | 540,632 | G→T | 13.2% | C23F (TGC→TTC) | ybbY → | putative uracil/xanthine transporter |
| RA | 693,429 | T→A | 10.7% | intergenic (‑51/+102) | ybeZ ← / ← miaB | heat shock protein, putative NTPase; PhoH‑like protein/tRNA‑i(6)A37 methylthiotransferase |
| RA | 706,050 | Δ1 bp | 6.0% | intergenic (+160/‑43) | nagE → / → glnS | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components/glutamyl‑tRNA synthetase |
| RA | 740,177 | A→G | 9.9% | E224G (GAG→GGG) | phr → | deoxyribodipyrimidine photolyase, FAD‑binding |
| RA | 753,618 | T→G | 10.3% | H284P (CAC→CCC) | gltA ← | citrate synthase |
| RA | 758,596 | G→C | 17.0% | intergenic (+191/‑110) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 806,020 | A→C | 8.5% | V421G (GTG→GGG) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 816,752 | T→A | 11.6% | intergenic (‑105/‑292) | ybhK ← / → moaA | putative CofD superfamily transferase/molybdopterin biosynthesis protein A |
| RA | 845,227 | A→C | 19.3% | V85G (GTG→GGG) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 861,215 | G→C | 12.9% | R464R (CGC→CGG) | ybiW ← | putative pyruvate formate lyase |
| RA | 910,397 | T→C | 13.6% | E218G (GAG→GGG) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| RA | 910,811 | T→G | 22.8% | H80P (CAC→CCC) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| RA | 921,692 | T→G | 13.7% | V449G (GTG→GGG) | macB → | macrolide ABC transporter peremase/ATPase |
| RA | 954,388 | C→T | 23.8% | A27T (GCA→ACA) | focA ← | formate channel |
| RA | 964,532 | A→G | 5.9% | G71G (GGA→GGG) | ycaI → | ComEC family inner membrane protein |
| RA | 973,698 | A→G | 13.4% | G54G (GGA→GGG) | smtA → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 974,068 | C→A | 11.1% | R178R (CGG→AGG) | smtA → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 1,030,269 | C→T | 17.6% | S69F (TCT→TTT) | yccX → | weak acylphosphatase |
| RA | 1,058,486 | T→C | 16.8% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,078,659 | T→G | 17.8% | H75P (CAC→CCC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,136,671 | T→G | 12.7% | V133G (GTG→GGG) | flgI → | putative flagellar basal body protein |
| RA | 1,196,305 | C→T | 63.9% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,213,890 | A→T | 12.2% | I57K (ATA→AAA) | bluR ← | repressor of blue light‑responsive genes |
| RA | 1,239,855 | A→G | 17.6% | E326G (GAG→GGG) | dadX → | alanine racemase, catabolic, PLP‑binding |
| RA | 1,241,337 | A→C | 19.5% | G245G (GGT→GGG) | cvrA ← | putative cation/proton antiporter |
| RA | 1,251,973 | T→C | 15.9% | L303P (CTC→CCC) | dhaR → | dhaKLM operon transcription activator |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,365,542 | T→G | 9.7% | intergenic (+30/‑8) | puuB → / → puuE | gamma‑glutamylputrescine oxidoreductase/4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 1,366,268 | T→G | 13.2% | V240G (GTG→GGG) | puuE → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 1,445,981 | T→G | 22.0% | G34G (GGT→GGG) | ydbL → | DUF1318 family protein |
| RA | 1,455,846 | A→C | 14.5% | H228P (CAC→CCC) | paaC → | ring 1,2‑phenylacetyl‑CoA epoxidase subunit |
| RA | 1,467,068 | T→G | 16.1% | pseudogene (1677/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,531,410 | C→A | 7.7% | pseudogene (86/315 nt) | yncI → | pseudogene |
| RA | 1,537,275 | T→C | 12.1% | E12G (GAG→GGG) | narW ← | nitrate reductase 2 (NRZ), delta subunit (assembly subunit) |
| RA | 1,543,530 | A→C | 15.0% | S177R (AGT→AGG) | narU ← | nitrate/nitrite transporter |
| RA | 1,614,336 | T→C | 14.7% | E123G (GAG→GGG) | sad ← | succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,668,252 | T→C | 10.3% | S105G (AGC→GGC) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| RA | 1,706,790 | C→A | 9.9% | T148K (ACG→AAG) | rsxB → | SoxR iron‑sulfur cluster reduction factor component; putative iron‑sulfur protein |
| RA | 1,710,100 | A→T | 8.4% | Y320F (TAT→TTT) | rsxD → | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| RA | 1,810,544 | A→G | 16.2% | S112G (AGC→GGC) | ydjM → | inner membrane protein regulated by LexA |
| RA | 1,823,068 | A→C | 12.2% | H204P (CAC→CCC) | nadE → | NAD synthetase, NH3/glutamine‑dependent |
| RA | 1,825,130 | G→T | 20.8% | intergenic (‑193/+10) | ves ← / ← spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,842,798 | T→G | 17.0% | V143G (GTG→GGG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,861,244 | A→C | 10.7% | V30G (GTG→GGG) | ydjL ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,879,473 | A→C | 21.0% | V38G (GTG→GGG) | yoaG ← | uncharacterized protein |
| RA | 1,923,379 | C→T | 16.7% | E110K (GAA→AAA) | yebY ← | DUF2511 family protein |
| RA | 1,955,112 | G→T | 10.9% | G632G (GGC→GGA) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,961,224 | T→G | 11.1% | V388G (GTG→GGG) | argS → | arginyl‑tRNA synthetase |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,041,503 | T→G | 12.1% | G43G (GGT→GGG) | zinT → | zinc and cadmium binding protein, periplasmic |
| RA | 2,097,266 | C→A | 12.3% | intergenic (+41/+55) | hisI → / ← wzzB | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,193,510 | A→C | 11.1% | V220G (GTG→GGG) | mrp ← | antiporter inner membrane protein |
| RA | 2,195,709 | C→G | 6.7% | R470R (CGC→CGG) | metG → | methionyl‑tRNA synthetase |
| RA | 2,253,949 | A→C | 10.2% | V66G (GTG→GGG) | nupX ← | nucleoside permease |
| RA | 2,274,349 | T→G | 21.8% | G57G (GGT→GGG) | yejB → | microcin C ABC transporter permease |
| RA | 2,282,167 | A→C | 13.6% | T512T (ACA→ACC) | yejH → | putative ATP‑dependent DNA or RNA helicase |
| RA | 2,285,462 | T→C | 9.3% | S363P (TCG→CCG) | yejM → | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| RA | 2,303,243 | A→G | 14.3% | S85S (TCT→TCC) | napF ← | ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA |
| RA | 2,321,376 | T→C | 7.4% | L445P (CTC→CCC) | atoS → | sensory histidine kinase in two‑component regulatory system with AtoC |
| RA | 2,398,640 | A→C | 11.3% | V509G (GTG→GGG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,503,025 | C→A | 9.8% | L487F (TTG→TTT) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,527,397 | T→G | 16.1% | V151G (GTG→GGG) | yfeH → | putative inorganic ion transporter |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 26.0% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,608,253 | C→G | 26.2% | A446G (GCG→GGG) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,659,475 | T→C | 10.3% | intergenic (‑8/+88) | hscB ← / ← iscA | HscA co‑chaperone, J domain‑containing protein Hsc56; IscU‑specific chaperone HscAB/FeS cluster assembly protein |
| RA | 2,714,233 | T→C | 10.3% | intergenic (+3/+206) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,777,459 | A→C | 11.3% | T3P (ACT→CCT) | ypjF → | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,778,040 | T→C | 12.5% | intergenic (+258/+106) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter |
| RA | 2,793,675 | T→G | 15.2% | V314G (GTG→GGG) | gabT → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 2,794,877 | A→G | 9.5% | I209V (ATC→GTC) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,815,007 | T→C | 13.4% | E478G (GAG→GGG) | gshA ← | glutamate‑cysteine ligase |
| RA | 2,820,043 | T→C | 15.8% | S657G (AGC→GGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,828,506 | T→G | 22.1% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,853,016 | A→C | 10.2% | H294P (CAC→CCC) | hypD → | hydrogenase maturation protein |
| RA | 2,880,919 | G→A | 6.1% | L44F (CTT→TTT) | casD ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| RA | 2,936,843 | T→C | 9.5% | S420S (TCT→TCC) | fucI → | L‑fucose isomerase |
| RA | 2,975,093 | T→G | 18.4% | T308P (ACT→CCT) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 2,978,166 | T→A | 26.2% | Y245F (TAT→TTT) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 2,978,476 | G→C | 11.9% | R142G (CGC→GGC) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 2,999,610 | A→T | 14.1% | R94R (CGT→CGA) | ygeR ← | LysM domain‑containing M23 family putative peptidase; septation lipoprotein |
| RA | 3,003,095 | A→G | 7.9% | E161G (GAG→GGG) | xdhB → | xanthine dehydrogenase, FAD‑binding subunit |
| RA | 3,027,731 | A→G | 14.6% | E204G (GAG→GGG) | ghxQ → | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| RA | 3,135,441 | T→G | 11.5% | T311P (ACC→CCC) | pitB ← | phosphate transporter |
| RA | 3,141,102 | T→C | 11.6% | D62G (GAT→GGT) | hybD ← | maturation protease for hydrogenase 2 |
| RA | 3,141,137 | G→C | 14.3% | G50G (GGC→GGG) | hybD ← | maturation protease for hydrogenase 2 |
| RA | 3,160,891 | T→C | 10.8% | S86G (AGC→GGC) | ygiQ ← | Radical SAM superfamily protein |
| RA | 3,162,372 | A→G | 9.1% | S100P (TCA→CCA) | ftsP ← | septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts) |
| RA | 3,184,576 | T→C | 15.3% | intergenic (‑110/‑264) | ribB ← / → yqiC | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/BMFP family putative fusogenic protein |
| RA | 3,209,974 | A→C | 12.9% | G190G (GGT→GGG) | tsaD ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein |
| RA | 3,220,858 | T→G | 14.7% | S455R (AGT→AGG) | patA → | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| RA | 3,277,426 | G→A | 11.3% | E30E (GAG→GAA) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,300,864 | T→C | 13.6% | E138G (GAG→GGG) | yhbT ← | SCP‑2 sterol transfer family protein |
| RA | 3,315,740 | A→C | 7.9% | V92G (GTG→GGG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,338,869 | T→C | 12.9% | E127G (GAG→GGG) | mlaE ← | ABC transporter maintaining OM lipid asymmetry, inner membrane permease protein |
| RA | 3,373,350 | A→G | 11.7% | L76P (CTC→CCC) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,437,054 | A→C | 11.6% | P179P (CCA→CCC) | trkA → | NAD‑binding component of TrK potassium transporter |
| RA | 3,487,702 | A→C | 13.4% | A304A (GCA→GCC) | yhfK → | putative transporter, FUSC superfamily inner membrane protein |
| RA | 3,499,609 | A→C | 22.9% | A54A (GCA→GCC) | yhfL → | small lipoprotein |
| RA | 3,532,535 | G→A | 8.4% | intergenic (‑96/‑283) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,532,555 | G→A | 9.7% | intergenic (‑116/‑263) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,534,880 | A→C | 10.4% | V330G (GTG→GGG) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,551,917 | A→C | 18.3% | V186G (GTG→GGG) | malP ← | maltodextrin phosphorylase |
| RA | 3,553,285 | T→G | 15.3% | G67G (GGT→GGG) | malT → | mal regulon transcriptional activator |
| RA | 3,560,455:1 | +G | 91.9% | 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 | 3,561,266 | G→C | 8.9% | R63G (CGT→GGT) | glpG ← | rhomboid intramembrane serine protease |
| RA | 3,563,346 | A→G | 13.3% | E445G (GAG→GGG) | glpD → | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding |
| RA | 3,697,740 | T→G | 15.7% | V428G (GTG→GGG) | bcsE → | cellulose production protein |
| RA | 3,741,500 | T→C | 6.6% | E28G (GAG→GGG) | ysaA ← | putative hydrogenase, 4Fe‑4S ferredoxin‑type component |
| RA | 3,784,900 | A→C | 13.2% | V39G (GTG→GGG) | yibN ← | putative rhodanese‑related sulfurtransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,820,320 | G→C | 13.3% | A284G (GCG→GGG) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,820,372 | A→C | 8.4% | W267G (TGG→GGG) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,833,715 | T→G | 12.9% | T275P (ACT→CCT) | yicI ← | putative alpha‑glucosidase |
| RA | 3,885,168 | T→C | 8.6% | P31P (CCT→CCC) | yidC → | membrane protein insertase |
| RA | 3,932,230 | C→T | 12.5% | I305I (ATC→ATT) | kup → | potassium transporter |
| RA | 3,932,686 | T→C | 10.6% | S457S (TCT→TCC) | kup → | potassium transporter |
| RA | 3,949,065 | T→C | 13.4% | E302G (GAG→GGG) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| RA | 3,952,893 | A→G | 11.5% | E137G (GAG→GGG) | ilvE → | branched‑chain amino acid aminotransferase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,011,490 | A→G | 9.2% | T139A (ACT→GCT) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,011,698 | T→G | 12.1% | V208G (GTG→GGG) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,022,323 | A→G | 12.5% | I36V (ATT→GTT) | tatB → | TatABCE protein translocation system subunit |
| RA | 4,022,863 | A→C | 7.4% | H43P (CAC→CCC) | tatC → | TatABCE protein translocation system subunit |
| RA | 4,065,580 | T→A | 14.1% | T63S (ACC→TCC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,073,924 | T→G | 12.8% | G62G (GGT→GGG) | yihV → | 6‑deoxy‑6‑sulphofructose kinase |
| RA | 4,101,255 | C→T | 9.8% | S149F (TCT→TTT) | sodA → | superoxide dismutase, Mn |
| RA | 4,103,607 | T→C | 15.4% | S457G (AGT→GGT) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,140,198 | T→G | 12.2% | H675P (CAC→CCC) | frwA ← | putative PTS enzyme: Hpr, enzyme I and II components |
| RA | 4,158,653 | T→G | 15.2% | V55G (GTG→GGG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,159,201 | A→C | 11.4% | T238P (ACT→CCT) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,160,854 | C→T | 44.0% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,195,535 | T→C | 9.1% | S189G (AGC→GGC) | thiC ← | phosphomethylpyrimidine synthase |
| RA | 4,246,567 | A→G | 10.7% | intergenic (‑148/‑217) | malE ← / → malK | maltose transporter subunit/maltose ABC transportor ATPase |
| RA | 4,277,560 | A→T | 14.1% | Y31F (TAT→TTT) | soxR → | redox‑sensitive transcriptional activator of soxS; autorepressor |
| RA | 4,295,700 | T→G | 26.9% | V407G (GTG→GGG) | gltP → | glutamate/aspartate:proton symporter |
| RA | 4,296,060 | C→T | 20.2% | 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 | 4,319,404 | A→C | 19.4% | V68G (GTG→GGG) | phnJ ← | carbon‑phosphorus lyase, SAM‑dependent |
| RA | 4,353,194 | T→G | 11.7% | intergenic (+113/+6) | ghoT → / ← lysU | toxin of GhoTS toxin‑antitoxin pair; membrane‑lytic protein; stimulator of persister cell formation/lysine tRNA synthetase, inducible |
| RA | 4,382,744 | A→G | 13.3% | G34G (GGA→GGG) | epmA → | Elongation Factor P Lys34 lysyltransferase |
| RA | 4,437,248 | A→G | 13.1% | E165G (GAG→GGG) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| RA | 4,440,952 | G→A | 10.5% | F88F (TTC→TTT) | ytfL ← | UPF0053 family inner membrane protein |
| RA | 4,443,934 | T→G | 11.2% | V518G (GTG→GGG) | tamA → | translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,444,674 | T→G | 13.3% | V188G (GTG→GGG) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,449,045 | T→G | 20.4% | intergenic (+3/+77) | chpB → / ← ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| RA | 4,452,852 | A→G | 30.3% | G94G (GGA→GGG) | ytfT → | putative sugar ABC transporter permease |
| RA | 4,455,978 | T→G | 10.6% | V65G (GTG→GGG) | mpl → | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase |
| RA | 4,458,424 | A→C | 19.7% | T156P (ACC→CCC) | pmbA → | putative antibiotic peptide MccB17 maturation peptidase |
| RA | 4,481,799 | T→C | 14.1% | E680G (GAG→GGG) | valS ← | valyl‑tRNA synthetase |
| RA | 4,485,026 | T→C | 12.8% | E309G (GAG→GGG) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,522,897 | A→G | 11.3% | S400P (TCC→CCC) | yjhG ← | putative dehydratase |
| RA | 4,542,117 | A→G | 10.8% | R27R (AGA→AGG) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,542,272 | A→G | 8.8% | E79G (GAG→GGG) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,549,430 | G→T | 10.7% | C208F (TGT→TTT) | fimH → | minor component of type 1 fimbriae |
| RA | 4,576,032 | T→C | 7.0% | pseudogene (2114/2937 nt) | yjiV → | pseudogene; conserved hypothetical protein |
| RA | 4,606,902 | A→G | 20.2% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| RA | 4,633,067 | T→G | 11.0% | V103G (GTG→GGG) | trpR → | transcriptional repressor, tryptophan‑binding |
| RA | 4,638,873 | A→T | 10.3% | L232F (TTA→TTT) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 954468 | 954800 | 333 | 32 [31] | [27] 32 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| * | * | ÷ | NC_000913 | 2470080 | 2470506 | 427 | 34 [28] | [30] 32 | [gtrS] | [gtrS] |
| * | * | ÷ | NC_000913 | 4233739 | 4235491 | 1753 | 33 [31] | [31] 33 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.210) | 90 (0.920) | 59/394 | NT | 83.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.220) | 106 (1.080) | 60/394 | NT | 85.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 22 (0.210) | 20/418 | 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 | = 1978502 | 0 (0.000) | 45 (0.440) | 37/410 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 4110716 | NA (NA) | 3 (0.030) | 3/408 | NT | NA | noncoding (7/19 nt) | REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 4110721 | NA (NA) | noncoding (12/19 nt) | REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP303 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||