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 | 3,336 | G→T | 24.4% | G179V (GGG→GTG) | thrB → | homoserine kinase |
| RA | 34,502 | G→T | 16.2% | G68V (GGG→GTG) | caiF → | cai operon transcriptional activator |
| RA | 63,846 | G→T | 12.5% | A645A (GCC→GCA) | polB ← | DNA polymerase II |
| RA | 72,406 | G→T | 12.1% | L461M (CTG→ATG) | sgrR ← | transcriptional DNA‑binding transcriptional activator of sgrS sRNA |
| RA | 92,346 | G→T | 24.0% | G404C (GGC→TGC) | murF → | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| RA | 100,246 | C→T | 11.8% | T202M (ACG→ATG) | ftsQ → | divisome assembly protein, membrane anchored protein involved in growth of wall at septum |
| RA | 102,375 | G→T | 18.3% | G195V (GGT→GTT) | ftsZ → | GTP‑binding tubulin‑like cell division protein |
| RA | 108,846 | G→C | 36.4% | P81A (CCT→GCT) | zapD ← | FtsZ stabilizer |
| RA | 164,694 | G→C | 28.6% | E242Q (GAA→CAA) | fhuA → | ferrichrome outer membrane transporter |
| RA | 164,697 | Δ1 bp | 28.6% | coding (727/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| RA | 164,698 | A→T | 28.6% | E243V (GAG→GTG) | fhuA → | ferrichrome outer membrane transporter |
| RA | 169,317 | G→T | 8.7% | G457C (GGC→TGC) | fhuB → | fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components |
| RA | 186,083 | G→T | 14.3% | intergenic (‑90/‑116) | map ← / → tff | methionine aminopeptidase/novel sRNA, function unknown |
| RA | 205,422 | C→T | 11.8% | I105I (ATC→ATT) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| RA | 217,981 | G→T | 15.3% | P43Q (CCG→CAG) | metI ← | DL‑methionine transporter subunit |
| RA | 221,373:1 | +G | 15.9% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 15.9% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 15.9% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 15.9% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 16.7% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 16.7% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 16.7% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 16.7% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 16.6% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 16.7% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 16.4% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 17.9% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 21.2% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 21.2% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 30.0% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 263,966 | G→T | 12.2% | R236R (CGG→AGG) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 274,938 | T→A | 18.2% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 309,925 | Δ1 bp | 26.7% | intergenic (‑409/‑143) | ykgP ← / → eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified |
| RA | 309,926 | Δ1 bp | 26.7% | intergenic (‑410/‑142) | ykgP ← / → eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified |
| RA | 309,927 | Δ1 bp | 26.7% | intergenic (‑411/‑141) | ykgP ← / → eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified |
| RA | 383,954 | A→C | 16.5% | Q235P (CAG→CCG) | tauD → | taurine dioxygenase, 2‑oxoglutarate‑dependent |
| RA | 398,423 | C→A | 18.2% | G407G (GGC→GGA) | phoA → | bacterial alkaline phosphatase |
| RA | 470,183 | C→T | 14.3% | P145P (CCG→CCA) | tesB ← | acyl‑CoA thioesterase 2 |
| RA | 497,341 | G→T | 7.4% | R452S (CGT→AGT) | ybaL ← | inner membrane putative NAD(P)‑binding transporter |
| RA | 498,188 | G→T | 12.9% | P169P (CCC→CCA) | ybaL ← | inner membrane putative NAD(P)‑binding transporter |
| RA | 504,115 | G→T | 15.5% | intergenic (+100/+216) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator/copper transporter |
| RA | 504,928 | C→G | 15.4% | A636A (GCG→GCC) | copA ← | copper transporter |
| RA | 504,929:1 | +C | 15.4% | coding (1907/2505 nt) | copA ← | copper transporter |
| RA | 525,408 | A→T | 11.8% | pseudogene (65/357 nt) | ylbG ← | pseudogene, DNA‑binding transcriptional regulator homology |
| RA | 545,098 | C→A | 40.5% | P6T (CCT→ACT) | ylbF → | putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein |
| RA | 621,365 | G→T | 16.0% | W342L (TGG→TTG) | entC → | isochorismate synthase 1 |
| RA | 641,105 | G→T | 14.5% | T311N (ACT→AAT) | citT ← | citrate:succinate antiporter |
| RA | 709,367 | C→A | 27.3% | T118T (ACC→ACA) | pgm → | phosphoglucomutase |
| RA | 717,291 | C→A | 21.2% | G860G (GGG→GGT) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 725,992 | C→A | 6.7% | P318P (CCC→CCA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,100 | A→G | 10.7% | R354R (CGA→CGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,110 | T→C | 6.2% | C358R (TGT→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 741,049 | G→A | 10.8% | E143E (GAG→GAA) | ybgL → | UPF0271 family protein |
| RA | 764,985 | C→A | 18.4% | R518R (CGG→AGG) | mngB → | alpha‑mannosidase |
| RA | 774,198 | C→A | 11.8% | Q335K (CAG→AAG) | tolB → | periplasmic protein |
| RA | 817,379 | G→T | 13.8% | I192I (ATC→ATA) | ybhN ← | UPF0104 family inner membrane protein |
| RA | 821,941 | C→T | 11.1% | P256P (CCG→CCA) | ybhS ← | inner membrane putative ABC superfamily transporter permease |
| RA | 921,462 | C→T | 22.2% | intergenic (‑35/+219) | serW ← / ← infA | tRNA‑Ser/translation initiation factor IF‑1 |
| RA | 989,052 | C→A | 16.7% | R150L (CGA→CTA) | ssuB ← | alkanesulfonate transporter subunit |
| RA | 989,067 | C→A | 16.7% | R145I (AGA→ATA) | ssuB ← | alkanesulfonate transporter subunit |
| RA | 1,016,418 | C→A | 100% | intergenic (‑43/‑176) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| RA | 1,050,927 | G→T | 12.1% | L236L (CTC→CTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,052,041 | G→T | 14.3% | G109C (GGT→TGT) | torT → | periplasmic sensory protein associated with the TorRS two‑component regulatory system |
| RA | 1,108,650 | C→A | 14.4% | R778S (CGT→AGT) | opgH → | membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,158,148 | G→T | 19.5% | G19W (GGG→TGG) | lpoB → | OM lipoprotein stimulator of MrcB transpeptidase |
| RA | 1,282,287 | T→A | 17.5% | intergenic (+305/+235) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,288,276 | C→A | 14.0% | V35F (GTT→TTT) | hns ← | global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,310,303 | C→A | 22.2% | intergenic (‑11/+370) | yciG ← / ← trpA | KGG family protein/tryptophan synthase, alpha subunit |
| RA | 1,378,274 | C→A | 14.9% | intergenic (‑56/‑100) | ycjW ← / → ycjX | LacI family putative transcriptional repressor/DUF463 family protein, putative P‑loop NTPase |
| RA | 1,392,255 | G→A | 28.5% | L209L (CTG→TTG) | uspE ← | stress‑induced protein |
| RA | 1,415,096 | G→T | 17.5% | Q52H (CAG→CAT) | ydaT → | Rac prophage; uncharacterized protein |
| RA | 1,530,041 | G→T | 28.8% | F25L (TTC→TTA) | yddE ← | PhzC‑PhzF family protein |
| RA | 1,531,796 | G→T | 9.6% | Q439K (CAG→AAG) | narY ← | nitrate reductase 2 (NRZ), beta subunit |
| RA | 1,651,091 | C→A | 15.5% | V208V (GTG→GTT) | ynfC ← | UPF0257 family lipoprotein |
| RA | 1,661,618 | G→T | 14.8% | R402S (CGT→AGT) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| RA | 1,665,109 | G→T | 22.2% | W385L (TGG→TTG) | ynfM → | putative arabinose efflux transporter |
| RA | 1,678,059 | C→A | 23.5% | L307L (CTC→CTA) | rstB → | sensory histidine kinase of RstAB two‑component system, low Mg‑responsive via PhoQP |
| RA | 1,721,888 | C→A | 7.4% | R325S (CGT→AGT) | nemA → | chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme |
| RA | 1,759,661 | C→A | 14.2% | E77* (GAG→TAG) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| RA | 1,778,222 | G→T | 13.4% | G312V (GGA→GTA) | fadK → | short chain acyl‑CoA synthetase, anaerobic |
| RA | 1,861,156 | C→T | 16.0% | intergenic (‑427/‑9) | mipA ← / → yeaG | scaffolding protein for murein synthesizing machinery/protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,861,588 | A→G | 16.7% | S142G (AGC→GGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,871,247 | C→T | 14.8% | R28C (CGC→TGC) | yeaO → | DUF488 family protein |
| RA | 1,892,493 | G→T | 22.5% | M435I (ATG→ATT) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,906,114 | G→A | 9.3% | A240A (GCC→GCT) | htpX ← | putative endopeptidase |
| JC JC | 1,972,762 | IS5 (–) +4 bp | 93.1% | intergenic (‑308/‑469) | flhD ← / → uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| RA | 1,991,827 | A→G | 26.7% | L45P (CTG→CCG) | yecS ← | ABC family putative inner membrane permease |
| RA | 2,015,830 | G→T | 20.2% | G161* (GGA→TGA) | fliP → | flagellar biosynthesis protein |
| RA | 2,066,948 | G→T | 25.0% | V643V (GTG→GTT) | flu → | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,111,960:1 | +T | 22.2% | intergenic (‑75/+201) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,963 | A→C | 24.0% | intergenic (‑78/+198) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,981 | A→G | 35.3% | intergenic (‑96/+180) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,985 | G→A | 35.4% | intergenic (‑100/+176) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,989 | C→T | 37.5% | intergenic (‑104/+172) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,991 | A→T | 37.5% | intergenic (‑106/+170) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,111,994 | Δ1 bp | 37.5% | intergenic (‑109/+167) | wcaK ← / ← wzxC | colanic acid biosynthesis protein/putative colanic acid exporter |
| RA | 2,225,607 | G→T | 14.9% | A95A (GCG→GCT) | cdd → | cytidine/deoxycytidine deaminase |
| RA | 2,227,125 | C→A | 13.1% | P16Q (CCG→CAG) | yeiS → | DUF2542 family protein |
| RA | 2,233,967 | G→T | 9.8% | intergenic (‑140/+140) | mglB ← / ← galS | methyl‑galactoside transporter subunit/galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,238,045 | G→T | 11.2% | Q219H (CAG→CAT) | yeiG → | S‑formylglutathione hydrolase |
| RA | 2,244,113 | G→T | 15.6% | L306L (CTG→CTT) | yeiH → | UPF0324 family inner membrane protein |
| RA | 2,263,817 | G→T | 17.4% | M120I (ATG→ATT) | mepS → | murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein |
| RA | 2,269,365 | G→T | 11.5% | W205L (TGG→TTG) | yejE → | microcin C transporter YejABEF, permease subunit; ABC family |
| RA | 2,296,021 | G→T | 9.8% | P71Q (CCG→CAG) | napA ← | nitrate reductase, periplasmic, large subunit |
| RA | 2,326,819 | G→T | 14.9% | pseudogene (1063/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,332,758 | C→T | 9.7% | V48I (GTA→ATA) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,375,419 | G→T | 11.8% | W111C (TGG→TGT) | rbn → | RNase BN, tRNA processing enzyme |
| RA | 2,394,903 | C→T | 13.8% | G44G (GGG→GGA) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,409,821 | G→T | 25.2% | P532P (CCG→CCT) | pta → | phosphate acetyltransferase |
| RA | 2,433,703 | G→T | 11.7% | intergenic (‑104/+161) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,435,149 | C→A | 11.1% | intergenic (‑65/‑94) | fabB ← / → mnmC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,458,434 | C→A | 11.5% | C18F (TGT→TTT) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,483,597 | G→A | 25.0% | G23G (GGC→GGT) | yfdV ← | putative transporter |
| RA | 2,497,314 | C→A | 30.1% | E217D (GAG→GAT) | fryA ← | putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component |
| RA | 2,630,904 | C→A | 12.5% | E370* (GAA→TAA) | bamB ← | BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,711,246 | C→A | 17.1% | M214I (ATG→ATT) | yfiF ← | putative methyltransferase |
| RA | 2,712,898 | C→A | 25.0% | P106Q (CCA→CAA) | yfiP → | DTW domain protein |
| RA | 2,717,540 | G→T | 10.5% | M18I (ATG→ATT) | yfiM → | putative lipoprotein |
| RA | 2,726,602 | C→A | 12.6% | V311L (GTA→TTA) | clpB ← | protein disaggregation chaperone |
| RA | 2,735,641 | C→T | 9.1% | I136I (ATC→ATT) | yfiR → | putative periplasmic inhibitor of YfiN activity |
| RA | 2,812,350 | C→A | 22.2% | Q52H (CAG→CAT) | csrA ← | pleiotropic regulatory protein for carbon source metabolism |
| RA | 2,853,031 | C→A | 18.2% | intergenic (+18/‑88) | mutS → / → pphB | methyl‑directed mismatch repair protein/serine/threonine‑specific protein phosphatase 2 |
| RA | 2,858,407 | C→A | 18.3% | intergenic (+36/‑53) | ygbM → / → ygbN | putative hydroxypyruvate isomerase/putative transporter |
| RA | 2,902,577 | G→T | 7.7% | S150Y (TCC→TAC) | pyrG ← | CTP synthetase |
| RA | 2,946,848 | C→A | 19.0% | G839W (GGG→TGG) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 2,976,007 | T→C | 10.5% | Q204R (CAA→CGA) | kduD ← | hexuronate dehydrogenase; hexuronate utilization in high osmolarity |
| RA | 3,001,506 | C→T | 10.0% | A213V (GCC→GTC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,018,951 | C→A | 19.2% | P414P (CCC→CCA) | xanQ → | xanthine permease |
| RA | 3,038,704:1 | +T | 20.0% | coding (557/744 nt) | ygfF ← | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 3,049,807 | C→T | 12.5% | P70S (CCC→TCC) | fau → | 5‑formyltetrahydrofolate cyclo‑ligase family protein |
| RA | 3,061,418 | G→T | 8.5% | L8M (CTG→ATG) | yggE ← | oxidative stress defense protein |
| RA | 3,111,438 | C→A | 14.4% | G345V (GGG→GTG) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,126,064 | G→T | 22.4% | Q170K (CAA→AAA) | yghR ← | putative ATP‑binding protein |
| RA | 3,154,808 | G→T | 10.8% | N407K (AAC→AAA) | ftsP ← | septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts) |
| RA | 3,176,768 | C→A | 28.6% | intergenic (+86/+404) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,196,432 | C→T | 9.7% | R395W (CGG→TGG) | cca → | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase |
| RA | 3,231,393 | G→T | 10.2% | G242C (GGC→TGC) | ygjR → | putative NAD(P)‑dependent dehydrogenase |
| RA | 3,309,253 | C→A | 8.7% | E41* (GAG→TAG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,316,508 | C→A | 14.3% | D308Y (GAC→TAC) | glmM ← | phosphoglucosamine mutase |
| RA | 3,414,868 | G→T | 16.6% | W62L (TGG→TTG) | yhdY → | putative amino‑acid transporter subunit |
| RA | 3,416,890 | T→G | 14.7% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 13.1% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,474,724 | C→A | 30.0% | P26H (CCT→CAT) | yheS → | putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | 3,490,893 | G→A | 14.2% | A178T (GCG→ACG) | nirC → | nitrite transporter |
| RA | 3,496,562 | G→T | 7.4% | D13Y (GAT→TAT) | frlD → | fructoselysine 6‑kinase |
| RA | 3,579,440 | C→A | 19.1% | A248A (GCG→GCT) | ggt ← | gamma‑glutamyltranspeptidase |
| RA | 3,609,035 | G→T | 12.1% | M145I (ATG→ATT) | nikB → | nickel transporter subunit |
| RA | 3,629,574 | C→T | 12.5% | S399S (TCG→TCA) | yhiN ← | putative oxidoreductase |
| RA | 3,650,686 | T→A | 9.6% | I111N (ATT→AAT) | hdeD → | acid‑resistance membrane protein |
| RA | 3,663,315 | G→T | 28.8% | E122* (GAG→TAG) | treF → | cytoplasmic trehalase |
| RA | 3,669,503 | G→T | 16.0% | intergenic (+35/+147) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,703,833 | C→A | 18.2% | M1M (ATG→ATT) † | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,707,269 | T→C | 26.0% | G86G (GGT→GGC) | yiaC → | putative acyl‑CoA transferase |
| RA | 3,714,085 | A→T | 8.2% | N16Y (AAT→TAT) | insJ → | IS150 transposase A |
| RA | 3,849,445 | A→G | 12.5% | L75L (TTA→CTA) | yidH ← | DUF202 family inner membrane protein |
| RA | 3,854,666 | C→A | 15.0% | pseudogene (682/815 nt) | glvG ← | pseudogene; probable 6‑phospho‑beta‑glucosidase |
| RA | 3,875,471 | G→T | 16.8% | P71T (CCG→ACG) | dnaN ← | DNA polymerase III, beta subunit |
| RA | 3,888,770 | A→G | 100% | I400I (ATT→ATC) | purP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 4,042,956 | C→T | 10.5% | I877I (ATC→ATT) | polA → | fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease |
| RA | 4,053,103 | G→T | 9.5% | R446L (CGT→CTT) | typA → | GTP‑binding protein |
| RA | 4,064,434 | G→T | 17.4% | P228Q (CCG→CAG) | yihS ← | aldose‑ketose isomerase; D‑mannose isomerase |
| RA | 4,140,689 | C→T | 10.2% | E780K (GAA→AAA) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,165,449 | C→T | 23.8% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 23.8% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,886 | G→A | 13.6% | K5K (AAG→AAA) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,178,209 | C→T | 22.2% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 100% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,230,082 | C→A | 33.7% | intergenic (‑99/‑171) | yjbT ← / → psiE | putative periplasmic protein/phosphate starvation inducible protein |
| RA | 4,268,329 | G→T | 20.0% | intergenic (‑335/‑78) | ryjA ← / → yjcD | novel sRNA, function unknown/inner membrane putative guanine permease |
| RA | 4,271,228 | G→A | 12.7% | A441T (GCA→ACA) | yjcE → | putative cation/proton antiporter |
| RA | 4,303,808 | C→A | 14.3% | P42T (CCT→ACT) | yjdP → | putative periplasmic protein |
| RA | 4,307,614 | C→A | 11.5% | A33A (GCG→GCT) | phnL ← | ribophosphonate triphosphate synthase subunit; putative ABC transporter ATP‑binding protein |
| RA | 4,329,084 | C→A | 19.4% | A419S (GCC→TCC) | adiA ← | arginine decarboxylase |
| RA | 4,351,354 | G→T | 20.0% | P133H (CCC→CAC) | cadC ← | cadBA operon transcriptional activator |
| RA | 4,402,865 | T→C | 13.9% | P7P (CCT→CCC) | yjfC → | ATP‑Grasp family ATPase |
| RA | 4,410,220 | G→T | 10.9% | G142W (GGG→TGG) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| RA | 4,420,655 | G→T | 12.5% | L325L (CTG→CTT) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,438,103 | G→T | 7.7% | intergenic (+51/‑161) | ytfP → / → chpS | GGCT‑like protein/antitoxin of the ChpBS toxin‑antitoxin system |
| RA | 4,475,065 | G→T | 25.8% | S235Y (TCC→TAC) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,527,581 | C→A | 9.1% | W334C (TGG→TGT) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,576,483 | G→T | 9.5% | pseudogene (150/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 80547 | 80627 | 81 | 3 [1] | [0] 3 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | CP009273 | 454338 | 455062 | 725 | 3 [0] | [1] 2 | [lon] | [lon] |
| * | * | ÷ | CP009273 | 455203 | 456677 | 1475 | 2 [1] | [1] 2 | lon | DNA‑binding ATP‑dependent protease La |
| * | * | ÷ | CP009273 | 502044 | 502060 | 17 | 2 [0] | [1] 2 | [ybaK] | [ybaK] |
| * | * | ÷ | CP009273 | 578902 | 579097 | 196 | 2 [0] | [0] 2 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 703352 | 703364 | 13 | 2 [0] | [0] 2 | glnS/chiP | glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars |
| * | * | ÷ | CP009273 | 796291 | 796362 | 72 | 2 [1] | [1] 2 | ybhH | putative PrpF family isomerase |
| * | * | ÷ | CP009273 | 830382 | 830394 | 13 | 2 [0] | [1] 3 | dinG | ATP‑dependent DNA helicase |
| * | * | ÷ | CP009273 | 1146180 | 1146194 | 15 | 3 [1] | [0] 3 | fabG | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase |
| * | * | ÷ | CP009273 | 1193235 | 1193251 | 17 | 3 [0] | [1] 2 | ymfE | e14 prophage; putative inner membrane protein |
| * | * | ÷ | CP009273 | 1230301 | 1230308 | 8 | 2 [0] | [1] 2 | nhaB/fadR | sodium:proton antiporter/fatty acid metabolism regulon transcriptional regulator |
| * | * | ÷ | CP009273 | 1524651 | 1524678 | 28 | 2 [0] | [0] 2 | [ydcD] | [ydcD] |
| * | * | ÷ | CP009273 | 1539022 | 1539044 | 23 | 2 [0] | [1] 2 | yddK | pseudogene, leucine‑rich protein; putative glycoportein |
| * | * | ÷ | CP009273 | 1557370 | 1557439 | 70 | 2 [0] | [1] 3 | ddpX/dosP | D‑ala‑D‑ala dipeptidase, Zn‑dependent/oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| * | * | ÷ | CP009273 | 1568021 | 1568073 | 53 | 3 [1] | [1] 4 | pqqL | putative periplasmic M16 family zinc metalloendopeptidase |
| * | * | ÷ | CP009273 | 1646672 | 1646724 | 53 | 5 [0] | [0] 4 | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related |
| * | * | ÷ | CP009273 | 1692508 | 1692546 | 39 | 5 [1] | [1] 5 | malI | transcriptional repressor of Mal regulon |
| * | * | ÷ | CP009273 | 1864765 | 1864866 | 102 | 3 [1] | [1] 2 | yeaI | putative membrane‑anchored diguanylate cyclase |
| * | * | ÷ | CP009273 | 1888083 | 1888098 | 16 | 8 [1] | [0] 4 | yoaB/yoaC | putative reactive intermediate deaminase/DUF1889 family protein |
| * | * | ÷ | CP009273 | 1990311 | 1990390 | 80 | 3 [1] | [0] 2 | [sdiA] | [sdiA] |
| * | * | ÷ | CP009273 | 2027278 | 2027435 | 158 | 2 [0] | [1] 2 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2096907 | 2096998 | 92 | 3 [1] | [1] 2 | wbbK | lipopolysaccharide biosynthesis protein |
| * | * | ÷ | CP009273 | 2462634 | 2462646 | 13 | 2 [0] | [0] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2462730 | 2462964 | 235 | 2 [0] | [1] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463629 | 2463879 | 251 | 2 [1] | [1] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2623001 | 2623013 | 13 | 2 [0] | [1] 2 | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| * | * | ÷ | CP009273 | 2767881 | 2768076 | 196 | 4 [1] | [0] 4 | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | * | ÷ | CP009273 | 2909984 | 2910013 | 30 | 2 [0] | [0] 2 | barA | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| * | * | ÷ | CP009273 | 2988464 | 2988541 | 78 | 5 [1] | [1] 2 | ygeK/ygeN | pseudogene; putative 2‑component transcriptional regulator/pseudogene |
| * | * | ÷ | CP009273 | 2989058 | 2989087 | 30 | 2 [1] | [1] 2 | ygeN | pseudogene |
| * | * | ÷ | CP009273 | 3406950 | 3406969 | 20 | 2 [0] | [1] 2 | acrS/acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| * | * | ÷ | CP009273 | 3629270 | 3629301 | 32 | 2 [0] | [1] 2 | yhiM/yhiN | acid resistance protein, inner membrane/putative oxidoreductase |
| * | * | ÷ | CP009273 | 3745266 | 3745346 | 81 | 5 [1] | [0] 2 | yiaT/yiaU | putative outer membrane protein/putative DNA‑binding transcriptional regulator |
| * | * | ÷ | CP009273 | 3762929 | 3763190 | 262 | 2 [1] | [1] 2 | [yibV]–yibV | [yibV],yibV |
| * | * | ÷ | CP009273 | 3792630 | 3792801 | 172 | 2 [1] | [1] 3 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | CP009273 | 3797657 | 3797719 | 63 | 3 [0] | [0] 2 | waaS | lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | CP009273 | 3798255 | 3798456 | 202 | 2 [1] | [1] 3 | waaS | lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | CP009273 | 3830068 | 3830237 | 170 | 3 [1] | [1] 2 | yicT/setC | pseudogene/putative arabinose efflux transporter |
| * | * | ÷ | CP009273 | 4037430 | 4037540 | 111 | 3 [1] | [0] 2 | dsbA/yihF | periplasmic protein disulfide isomerase I/DUF945 family protein |
| * | * | ÷ | CP009273 | 4294341 | 4294386 | 46 | 3 [0] | [1] 2 | ytcA/yjcS | putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein |
| * | * | ÷ | CP009273 | 4466693 | 4466841 | 149 | 2 [1] | [0] 2 | yjgL | uncharacterized protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 269817 | NA (NA) | 4 (0.190) | 3/246 | NT | NA | noncoding (1044/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 269869 = | NA (NA) | noncoding (992/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 360104 = | 5 (0.230) | 13 (0.600) | 7/248 | NT | 72.2% | 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 = | 15 (0.690) | 5 (0.270) | 3/216 | NT | 36.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 4 (0.210) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 13 (0.600) | 5 (0.270) | 3/216 | NT | 39.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 4 (0.210) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 4532499 = | 2 (0.090) | 5 (0.250) | 3/230 | NT | 40.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 13 (0.650) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||