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 | 17,728 | A→G | K80K (AAA→AAG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 86,547 | T→A | D306E (GAT→GAA) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 159,035 | A→G | V31A (GTG→GCG) | pcnB ← | poly(A) polymerase I |
| RA | 229,044 | (T)8→7 | intergenic (+40/‑123) | aspU → / → dkgB | tRNA‑Asp/methylglyoxal reductase DkgB |
| RA | 321,498 | T→C | intergenic (+417/‑110) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 345,973 | (G)5→4 | coding (365/672 nt) | yahN ← | putative amino acid exporter |
| RA | 368,372 | G→A | R17C (CGC→TGC) | mhpR ← | DNA‑binding transcriptional activator MhpR |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 391,703 | (G)6→5 | pseudogene (1453/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 404,504 | A→G | I268V (ATT→GTT) | dgcC → | diguanylate cyclase DgcC |
| RA | 424,940 | G→A | intergenic (‑22/‑71) | acpH ← / → queA | acyl carrier protein phosphodiesterase/tRNA preQ1(34) S‑adenosylmethionine ribosyltransferase‑isomerase |
| RA | 511,810 | A→G | D57G (GAC→GGC) | glsA → | glutaminase 1 |
| RA | 565,791 | C→T | C63Y (TGC→TAC) | intD ← | DLP12 prophage; putative integrase |
| RA | 593,034 | A→G | L49L (TTG→CTG) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 618,411 | C→T | A53V (GCA→GTA) | fepE → | polysaccharide co‑polymerase family protein FepE |
| RA | 665,013 | C→T | D60N (GAT→AAT) | rlpA ← | rare lipoprotein RlpA |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
| RA | 766,957 | (G)6→7 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 785,094 | T→C | D75G (GAT→GGT) | ybgS ← | PF13985 family protein YbgS |
| RA | 849,636 | (C)5→4 | coding (462/888 nt) | rhtA ← | L‑threonine/L‑homoserine exporter |
| RA | 907,383 | T→C | K300K (AAA→AAG) | ybjT ← | putative NAD(P)‑dependent oxidoreductase YbjT |
| RA | 977,944 | C→T | A540V (GCA→GTA) | mukB → | chromosome partitioning protein MukB |
| RA | 985,846 | (A)8→7 | intergenic (‑137/+48) | aspC ← / ← ompF | aspartate aminotransferase/outer membrane porin F |
| RA | 1,023,649 | C→T | A79T (GCC→ACC) | yccS ← | putative transporter YccS |
| RA | 1,029,161 | A→G | L270P (CTG→CCG) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,053,140 | A→G | W75R (TGG→CGG) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,159,200 | C→T | G444G (GGC→GGT) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,188,128 | T→C | D38G (GAC→GGC) | roxA ← | ribosomal protein‑arginine oxygenase |
| RA | 1,198,319 | T→C | intergenic (‑82/‑376) | ymfE ← / → lit | e14 prophage; uncharacterized protein YmfE/e14 prophage; cell death peptidase Lit |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,224,832 | T→C | H177R (CAC→CGC) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,259,984 | A→G | S274P (TCT→CCT) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | 1,334,189 | T→C | I112T (ATC→ACC) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,387,240 | T→C | V174A (GTC→GCC) | tyrR → | DNA‑binding transcriptional dual regulator TyrR |
| RA | 1,418,141 | A→G | I30T (ATT→ACT) | kilR ← | Rac prophage; inhibitor of FtsZ, killing protein |
| RA | 1,503,246 | T→C | intergenic (+121/‑471) | ydcL → / → insQ | DUF3313 domain‑containing lipoprotein YdcL/putative insertion element transposase InsQ |
| RA | 1,505,736 | A→G | R115R (CGT→CGC) | ydcO ← | putative transport protein YdcO |
| RA | 1,585,257 | G→A | G410G (GGC→GGT) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,606,098 | T→C | intergenic (+25/‑2) | lsrB → / → lsrF | Autoinducer‑2 ABC transporter periplasmic binding protein/3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| RA | 1,634,965 | T→C | T295A (ACC→GCC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,808,838 | +C | coding (396/537 nt) | yniB ← | uncharacterized protein YniB |
| RA | 1,864,358 | G→A | G170D (GGT→GAT) | yeaD → | putative aldose 1‑epimerase YeaD |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,879,162 | T→C | T32A (ACT→GCT) | yeaQ ← | PF04226 family protein YeaQ |
| RA | 1,880,319 | T→C | P147P (CCA→CCG) | leuE ← | leucine exporter |
| RA | 2,027,073 | T→C | E315E (GAA→GAG) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,043,416 | T→C | intergenic (+518/+52) | yodB → / ← serU | putative cytochrome/tRNA‑Ser |
| RA | 2,106,518 | (C)6→7 | coding (709/1167 nt) | wbbH ← | putative O‑antigen polymerase |
| RA | 2,145,905 | G→A | S880S (TCG→TCA) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,154,123 | C→T | A36A (GCC→GCT) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,162,178 | G→A | V239M (GTG→ATG) | mdtD → | putative multidrug efflux pump MdtD |
| RA | 2,167,830 | (T)7→6 | intergenic (‑10/+159) | yegZ ← / ← yegR | phage protein D/uncharacterized protein YegR |
| RA | 2,203,158 | T→C | R960R (CGT→CGC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,207,355 | T→C | L554P (CTG→CCG) | yehM → | putative YehN |
| RA | 2,217,147 | (G)5→6 | coding (261/927 nt) | yehX ← | glycine betaine ABC transporter ATP binding subunit YehX |
| RA | 2,294,363 | T→C | Y181C (TAC→TGC) | ccmF ← | holocytochrome c synthetase membrane subunit CcmF |
| RA | 2,423,798 | G→A | Q238* (CAG→TAG) | hisP ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit |
| RA | 2,431,730 | G→A | H405Y (CAC→TAC) | folC ← | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase |
| RA | 2,438,214 | G→A | A89T (GCC→ACC) | flk → | putative flagella assembly protein |
| RA | 2,529,317 | A→G | V287A (GTG→GCG) | ligA ← | DNA ligase |
| RA | 2,530,354 | C→T | D294N (GAT→AAT) | zipA ← | cell division protein ZipA |
| RA | 2,562,867 | T→C | V115A (GTG→GCG) | yffP → | CPZ‑55 prophage; uncharacterized protein YffP |
| RA | 2,580,140 | G→A | A169T (GCA→ACA) | tktB → | transketolase 2 |
| RA | 2,589,492 | G→A | W633* (TGG→TAG) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,648,051 | G→A | L1413F (CTT→TTT) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,717,416 | G→A | M221I (ATG→ATA) | ung → | uracil‑DNA glycosylase |
| RA | 2,734,921 | G→A | A38A (GCC→GCT) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,767,507 | (C)7→8 | intergenic (+152/‑203) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,976,742 | C→T | N48N (AAC→AAT) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 2,981,785 | G→A | A133V (GCT→GTT) | araE ← | arabinose:H(+) symporter |
| RA | 3,024,705 | T→C | S119P (TCG→CCG) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,032,280 | G→A | G305D (GGC→GAC) | uacT → | urate:H(+) symporter |
| RA | 3,079,151 | T→C | A60A (GCA→GCG) | cmtB ← | mannitol‑specific PTS enzyme IIA component CmtB |
| RA | 3,089,962 | G→A | A70T (GCT→ACT) | yggI → | conserved protein YggI |
| RA | 3,123,703 | A→G | F35L (TTC→CTC) | glcB ← | malate synthase G |
| RA | 3,157,712 | (C)6→7 | coding (63/927 nt) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,169,083 | T→C | N50S (AAC→AGC) | ygiV ← | DNA‑binding transcriptional repressor YgiV |
| RA | 3,267,773 | G→T | intergenic (+175/‑81) | tdcR → / → yhaB | DNA‑binding transcriptional activator TdcR/protein YhaB |
| RA | 3,276,110 | T→C | C277R (TGC→CGC) | garD → | galactarate dehydratase |
| RA | 3,302,336 | G→A | V284V (GTG→GTA) | yhbU → | putative peptidase YhbU |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,322,992 | T→C | H360R (CAC→CGC) | glmM ← | phosphoglucosamine mutase |
| RA | 3,338,141 | (C)5→6 | coding (321/552 nt) | mlaD ← | intermembrane phospholipid transport system, substrate binding protein MlaD |
| RA | 3,458,277 | T→C | V634A (GTG→GCG) | gspD → | Type II secretion system protein GspD |
| RA | 3,480,831 | T→C | T111A (ACC→GCC) | kefG ← | protein required for KefB activity |
| RA | 3,550,930 | A→G | V515A (GTG→GCG) | malP ← | maltodextrin phosphorylase |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,593,495 | G→A | P238S (CCG→TCG) | livG ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| RA | 3,648,327 | A→G | noncoding (34/84 nt) | agrB → | small RNA AgrB |
| RA | 3,668,886 | T→C | A101A (GCA→GCG) | ccp ← | cytochrome c peroxidase |
| RA | 3,810,786 | G→A | H123Y (CAT→TAT) | mutM ← | DNA‑formamidopyrimidine glycosylase |
| RA | 3,845,598 | T→C | G545G (GGT→GGC) | adeD → | adenine deaminase |
| RA | 4,114,038 | A→G | Y145Y (TAT→TAC) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,343,821 | (T)7→8 | coding (453/1422 nt) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,443,276 | A→G | T299A (ACC→GCC) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,453,435 | (G)5→4 | coding (865/1026 nt) | ytfT → | galactofuranose ABC transporter putative membrane subunit YtfT |
| RA | 4,490,614 | G→A | L176L (CTG→TTG) | idnR ← | DNA‑binding transcriptional dual regulator IdnR |
| RA | 4,500,711 | T→C | pseudogene (81/1199 nt) | yjgX ← | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment |
| RA | 4,564,437 | G→A | R85W (CGG→TGG) | yjiL ← | putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehdratase |
| RA | 4,581,520 | C→T | S510N (AGC→AAC) | hsdM ← | type I restriction enzyme EcoKI methyltransferase component |
| RA | 4,589,056 | (T)7→6 | coding (24/204 nt) | yjiX ← | conserved protein YjiX |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361202 | 361923 | 722 | 175 [171] | [171] 172 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856979 | 2857095 | 117 | 172 [169] | [0] 289 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423687–3424234 | 3424609–3424238 | 5–923 | 174 [166] | [171] 176 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 289 (1.000) | 273 (0.970) | 145/188 | 0.1 | 66.1% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||