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 | annotation | gene | description |
| RA | 567 | A→G | G77G (GGA→GGG) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 17,908 | A→G | V140V (GTA→GTG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 81,219 | T→C | N247S (AAC→AGC) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 119,796 | A→G | Q172Q (CAA→CAG) | ampE → | protein AmpE |
| RA | 207,342 | A→G | E739E (GAA→GAG) | dnaE → | DNA polymerase III subunit alpha |
| RA | 229,324 | G→A | G53D (GGC→GAC) | dkgB → | methylglyoxal reductase DkgB |
| RA | 232,955 | T→C | D334G (GAC→GGC) | mltD ← | membrane‑bound lytic murein transglycosylase D |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 305,455 | A→G | F455L (TTC→CTC) | ecpD ← | fimbrial adhesin EcpD |
| RA | 429,923 | C→T | A140V (GCA→GTA) | secF → | Sec translocon accessory complex subunit SecF |
| RA | 432,214 | T→C | intergenic (‑201/+98) | tsx ← / ← yajI | nucleoside‑specific channel‑forming protein Tsx/putative lipoprotein YajI |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 582,994 | G→A | A40A (GCG→GCA) | tfaX → | DLP12 prophage; protein TfaX |
| RA | 593,467 | T→C | D435G (GAC→GGC) | cusS ← | sensory histidine kinase CusS |
| RA | 733,427 | T→C | V1282A (GTC→GCC) | rhsC → | rhs element protein RhsC |
| RA | 773,325 | C→T | A95V (GCG→GTG) | cydB → | cytochrome bd‑I ubiquinol oxidase subunit II |
| RA | 778,178 | A→G | T147A (ACC→GCC) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 783,427 | T→C | W88R (TGG→CGG) | pnuC → | nicotinamide riboside transporter |
| RA | 868,422 | (C)8→9 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 984,021 | A→G | L124L (TTA→TTG) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,165,817 | A→G | intergenic (+132/‑268) | ycfP → / → ndh | UPF0227 protein YcfP/NADH:quinone oxidoreductase II |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,458,944 | A→G | Q227Q (CAA→CAG) | paaG → | putative ring 1,2‑epoxyphenylacetyl‑CoA isomerase (oxepin‑CoA forming) |
| RA | 1,462,292 | A→G | E56E (GAA→GAG) | paaK → | phenylacetate‑CoA ligase |
| RA | 1,474,919 | A→G | T233T (ACA→ACG) | pdxI → | pyridoxine 4‑dehydrogenase |
| RA | 1,529,344 | G→A | pseudogene (1455/2049 nt) | rhsE → | RhsE protein in rhs element |
| RA | 1,529,347 | G→A | pseudogene (1458/2049 nt) | rhsE → | RhsE protein in rhs element |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,549,590 | T→C | G730G (GGT→GGC) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,641,812 | A→G | intergenic (‑258/‑43) | cspB ← / → cspF | Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,750,738 | A→G | C92C (TGT→TGC) | ydhX ← | putative 4Fe‑4S ferredoxin‑type protein |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,963,934 | G→A | P373S (CCG→TCG) | flhA ← | flagellar biosynthesis protein FlhA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,031,309 | (T)6→7 | coding (1009/1419 nt) | dcm ← | DNA‑cytosine methyltransferase |
| RA | 2,037,230 | T→C | D308G (GAC→GGC) | hprS ← | sensory histidine kinase HprS |
| RA | 2,057,676 | (C)7→8 | intergenic (+102/+351) | yeeN → / ← asnW | putative transcriptional regulator YeeN/tRNA‑Asn |
| RA | 2,120,438 | (C)6→7 | coding (1117/1395 nt) | wcaJ ← | undecaprenyl‑phosphate glucose phosphotransferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,188,043 | (C)6→7 | coding (372/1035 nt) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,220,173 | A→T | I606N (ATC→AAC) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,330,624 | T→C | pseudogene (3779/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,363,298 | T→C | A112A (GCA→GCG) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,406,122 | A→G | Y174H (TAC→CAC) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,478,099 | G→C | A85P (GCC→CCC) | dsdX → | D‑serine transporter |
| RA | 2,497,944 | T→C | T118A (ACG→GCG) | alaC ← | glutamate‑‑pyruvate aminotransferase AlaC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,572,290 | G→A | A54V (GCC→GTC) | eutM ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,574,903 | G→A | A34V (GCC→GTC) | eutQ ← | putative ethanolamine utilization protein EutQ |
| RA | 2,624,198 | G→A | S385S (TCG→TCA) | ppk → | polyphosphate kinase |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,797,916 | T→C | Y133H (TAT→CAT) | ygaP → | thiosulfate sulfurtransferase YgaP |
| RA | 2,807,528 | G→A | A133T (GCA→ACA) | proX → | glycine betaine ABC transporter periplasmic binding protein ProX |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,904,216 | G→A | intergenic (+842/+531) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,918,991 | A→G | V132A (GTG→GCG) | gudD ← | D‑glucarate dehydratase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,007,944 | T→C | G145G (GGT→GGC) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,025,650 | G→A | A434T (GCT→ACT) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,033,306 | T→A | I81N (ATC→AAC) | idi → | isopentenyl‑diphosphate Delta‑isomerase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,154,296 | T→C | D308G (GAT→GGT) | yqhC ← | DNA‑binding transcriptional activator YqhC |
| RA | 3,159,005 | (T)7→8 | coding (2142/2220 nt) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,167,049 | T→C | T224A (ACT→GCT) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,215,455 | C→T | A7T (GCT→ACT) | mug ← | stationary phase mismatch/uracil DNA glycosylase |
| RA | 3,237,058 | T→C | G173G (GGT→GGC) | ygjQ → | DUF218 domain‑containing protein YgjQ |
| RA | 3,268,304 | (C)6→7 | coding (451/540 nt) | yhaB → | protein YhaB |
| RA | 3,350,184 | (C)7→8 | coding (276/654 nt) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,401,544 | T→C | S597G (AGC→GGC) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,405,411 | T→C | intergenic (+953/‑25) | yhdH → / → accB | acrylyl‑CoA reductase/biotin carboxyl carrier protein |
| RA | 3,532,835 | T→C | G6G (GGT→GGC) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,643,960 | T→C | Y408C (TAC→TGC) | prlC ← | oligopeptidase A |
| RA | 3,752,077 | T→C | V29A (GTA→GCA) | yiaU → | putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,878,946 | T→C | T392A (ACC→GCC) | gyrB ← | DNA gyrase subunit B |
| RA | 4,088,236 | G→A | A540A (GCC→GCT) | frvR ← | putative transcriptional regulator FrvR |
| MC JC | 4,102,102 | (AAG)3→2 | coding (413‑415/984 nt) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,102,818 | A→G | intergenic (+145/‑4) | kdgT → / → yiiM | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter/2‑amino‑6‑N‑hydroxylaminopurine resistance protein |
| RA | 4,232,278 | A→G | L319P (CTG→CCG) | lysC ← | aspartate kinase III |
| RA | 4,276,863 | A→G | I465V (ATC→GTC) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,485,626 | A→G | V109A (GTC→GCC) | pepA ← | aminopeptidase A/I |
| RA | 4,507,190 | T→C | intergenic (+81/‑7) | yjhE → / → insO | KpLE2 phage‑like element; putative membrane protein (pseudogene)/KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,640,121 | A→G | G62G (GGT→GGC) | arcA ← | DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1528439–1529174 | 1529306–1529287 | 114–868 | 14 [12] | [13] 15 | rhsE | RhsE protein in rhs element |
| * | * | ÷ | NC_000913 | 3423766–3424233 | 3424523–3424239 | 7–758 | 14 [13] | [11] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 78 (1.150) | 17 (0.280) | 16/244 | 1.9 | 20.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 64 (1.070) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 75 (1.140) | 50/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 123 (1.810) | 117 (1.730) | 56/274 | 0.1 | 64.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 5 (0.070) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 97 (1.430) | 61/276 | 0.1 | 99.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.010) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 32 (0.470) | 16 (0.250) | 13/258 | 2.6 | 26.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 61 (0.960) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 32 (0.470) | 22 (0.350) | 18/258 | 1.8 | 32.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 61 (0.960) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||