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 | 24,526 | A→G | V712V (GTA→GTG) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 41,373 | A→G | L187L (TTG→CTG) | caiT ← | L‑carnitine:gamma‑butyrobetaine antiporter |
| RA | 55,228 | A→G | Y628H (TAC→CAC) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 132,875 | A→G | T421A (ACC→GCC) | acnB → | hypothetical protein |
| RA | 143,016 | T→C | L80L (TTG→CTG) | yadG → | putative ABC transporter ATP‑binding protein YadG |
| RA | 144,903 | T→C | S109S (AGT→AGC) | yadI → | putative PTS enzyme IIA component YadI |
| RA | 214,929 | A→G | T33A (ACC→GCC) | arfB → | peptidyl‑tRNA hydrolase, ribosome rescue factor |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 348,483 | T→C | intergenic (‑40/‑199) | prpR ← / → prpB | DNA‑binding transcriptional dual regulator PrpR/2‑methylisocitrate lyase |
| RA | 371,179 | Δ1 bp | coding (903/945 nt) | mhpB → | 3‑carboxyethylcatechol 2,3‑dioxygenase |
| RA | 375,470 | T→C | R4R (CGT→CGC) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 396,655 | T→C | F6S (TTC→TCC) | sbmA → | peptide antibiotic/peptide nucleic acid transporter |
| RA | 445,912 | A→G | V252A (GTC→GCC) | yajR ← | putative major facilitator superfamily transport protein YajR |
| RA | 450,380 | C→T | A88T (GCG→ACG) | cyoB ← | cytochrome bo3 ubiquinol oxidase subunit 1 |
| RA | 479,289 | A→G | intergenic (‑38/+78) | ylaC ← / ← maa | putative inner membrane protein/maltose O‑acetyltransferase |
| RA | 523,311 | T→C | G17G (GGT→GGC) | rhsD → | protein RhsD |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 572,378 | A→G | Y4C (TAC→TGC) | ylcH → | DLP12 prophage; uncharacterized protein YlcH |
| RA | 622,253 | G→A | intergenic (‑64/‑47) | fepD ← / → entS | ferric enterobactin ABC transporter membrane subunit FebD/enterobactin exporter EntS |
| RA | 709,153 | A→G | T274A (ACC→GCC) | chiP → | chitobiose outer membrane channel |
| RA | 778,888 | A→G | A383A (GCA→GCG) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 789,332 | A→G | R216R (CGT→CGC) | galK ← | galactokinase |
| RA | 804,031 | A→G | T177A (ACC→GCC) | ybhJ → | putative hydratase YbhJ |
| RA | 876,549 | T→C | S405S (AGT→AGC) | dgcI → | putative diguanylate cyclase DgcI |
| RA | 884,588 | A→G | T306A (ACG→GCG) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| 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 | 945,476 | C→T | V28I (GTA→ATA) | ycaC ← | putative hydrolase |
| RA | 954,813 | (A)7→6 | intergenic (‑347/+59) | focA ← / ← ycaO | formate channel FocA/ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,036,051 | C→T | S94S (AGC→AGT) | hyaD → | putative hydrogenase 1 maturation protease HyaD |
| RA | 1,088,867 | G→A | Q331* (CAA→TAA) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,194,690 | G→T | L88M (CTG→ATG) | rluE ← | 23S rRNA pseudouridine(2457) synthase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,249,799 | A→G | V347A (GTC→GCC) | dhaK ← | dihydroxyacetone kinase subunit K |
| RA | 1,296,375 | A→G | F583L (TTC→CTC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,334,418 | A→G | E188E (GAA→GAG) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,338,156 | T→C | S776P (TCC→CCC) | acnA → | aconitate hydratase 1 |
| RA | 1,368,320 | A→G | K81R (AAA→AGA) | pspA → | phage shock protein A |
| RA | 1,385,351 | A→G | Y412C (TAT→TGT) | ycjX → | DUF463 domain‑containing protein YcjX |
| RA | 1,432,348 | T→C | A1100A (GCT→GCC) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,493,505 | A→G | S346G (AGC→GGC) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,505,587 | G→A | A165V (GCG→GTG) | ydcO ← | putative transport protein YdcO |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,585,785 | C→T | V234V (GTG→GTA) | ydeP ← | putative oxidoreductase YdeP |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,634,948 | A→G | A300A (GCT→GCC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,686,087 | T→C | T168A (ACA→GCA) | fumC ← | fumarase C |
| RA | 1,707,685 | C→T | T256I (ACC→ATC) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,802,361 | G→A | I70I (ATC→ATT) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,831,911 | T→C | I24M (ATA→ATG) | astC ← | succinylornithine transaminase |
| RA | 1,837,450 | G→A | W80* (TGG→TAG) | ynjC → | putative ABC transporter membrane subunit YnjC |
| RA | 1,868,951 | (G)6→7 | intergenic (+109/‑4) | yeaG → / → yeaH | protein kinase YeaG/DUF444 domain‑containing protein YeaH |
| 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 | 1,940,639 | C→T | G333S (GGT→AGT) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,947,694 | G→A | A153V (GCA→GTA) | yebC ← | putative transcriptional regulator YebC |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,985,520 | (C)5→6 | coding (609/990 nt) | araF ← | arabinose ABC transporter periplasmic binding protein |
| RA | 2,052,863 | A→G | pseudogene (466/1053 nt) | yeeL ← | putative glycosyltransferase, N‑terminal fragment |
| RA | 2,074,362 | (C)6→5 | coding (2824/3120 nt) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,147,052 | T→C | A163A (GCA→GCG) | alkA ← | DNA‑3‑methyladenine glycosylase 2 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,182,220 | G→A | Q188* (CAA→TAA) | yegW ← | putative DNA‑binding transcriptional regulator YegW |
| RA | 2,185,457 | G→A | intergenic (‑156/+67) | thiM ← / ← rcnR | hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR |
| RA | 2,197,183 | T→C | V237A (GTA→GCA) | yehF → | putative protein YehF |
| RA | 2,219,960 | T→C | N677S (AAC→AGC) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,338,063 | T→C | Q453R (CAG→CGG) | gyrA ← | DNA gyrase subunit A |
| RA | 2,354,450 | T→C | S62S (AGT→AGC) | glpB → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B |
| RA | 2,375,148 | G→A | T272M (ACG→ATG) | menC ← | o‑succinylbenzoate synthase |
| RA | 2,432,239 | T→C | D235G (GAC→GGC) | folC ← | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,504,447 | A→G | G13G (GGT→GGC) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,540,372 | (GC)5→4 | coding (442‑443/1098 nt) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,680,542 | G→A | A735V (GCG→GTG) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,720,013 | T→C | S21P (TCG→CCG) | patZ → | peptidyl‑lysine acetyltransferase |
| 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 | 2,772,160 | T→C | intergenic (‑6/+7) | yfjU ← / ← yfjV | CP4‑57 prophage; ArsC family protein YfjU/CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,826,470 | (A)8→9 | coding (79/960 nt) | srlE → | sorbitol‑specific PTS enzyme IIBC1 component |
| RA | 2,830,289 | T→C | N159N (AAT→AAC) | gutQ → | D‑arabinose 5‑phosphate isomerase GutQ |
| RA | 2,855,183 | A→G | L282L (TTA→TTG) | fhlA → | DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,933,613 | T→C | T26A (ACA→GCA) | fucA ← | L‑fuculose‑phosphate aldolase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,959,525 | A→G | R968R (CGT→CGC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,966,994 | C→T | A481T (GCG→ACG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,978,212 | C→T | V230I (GTT→ATT) | lysA ← | diaminopimelate decarboxylase |
| RA | 3,055,417 | A→G | Y10H (TAC→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,070,763 | T→C | Y161C (TAC→TGC) | fbaA ← | fructose‑bisphosphate aldolase class II |
| RA | 3,099,870 | T→C | T287A (ACT→GCT) | ansB ← | L‑asparaginase 2 |
| RA | 3,103,479 | G→A | G156E (GGG→GAG) | mutY → | adenine DNA glycosylase |
| RA | 3,197,894 | T→C | N583S (AAC→AGC) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,232,816 | T→C | P384P (CCT→CCC) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,282,014 | T→C | G13G (GGT→GGC) | agaS → | putative galactosamine‑6‑phosphate deaminase/isomerase |
| RA | 3,295,086 | G→A | G563S (GGT→AGT) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,301,141 | C→T | D46N (GAT→AAT) | yhbT ← | SCP2 domain‑containing protein YhbT |
| RA | 3,305,121 | T→C | T233A (ACG→GCG) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,317,948 | C→T | G20D (GGT→GAT) | rimP ← | ribosome maturation factor RimP |
| RA | 3,332,680 | (C)6→7 | coding (56/966 nt) | yhbE ← | inner membrane protein YhbE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,356,966 | (G)5→4 | coding (2242/4461 nt) | gltB → | glutamate synthase subunit GltB |
| RA | 3,376,571 | T→C | E69G (GAG→GGG) | sspB ← | ClpXP protease specificity‑enhancing factor |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,394,995 | C→T | V422I (GTT→ATT) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,446,372 | T→C | E58E (GAA→GAG) | rpsH ← | 30S ribosomal subunit protein S8 |
| RA | 3,450,057 | T→C | E59E (GAA→GAG) | rplV ← | 50S ribosomal subunit protein L22 |
| RA | 3,453,557 | G→A | A124V (GCC→GTC) | gspB ← | putative general secretion pathway protein B |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,561,338 | G→A | L39L (CTG→TTG) | glpG ← | rhomboid protease |
| RA | 3,619,269 | A→G | V26V (GTA→GTG) | rhsB → | rhs element protein RhsB |
| RA | 3,619,272 | T→C | R27R (CGT→CGC) | rhsB → | rhs element protein RhsB |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,830,613 | G→A | D53N (GAT→AAT) | yicH → | AsmA famly protein YicH |
| RA | 3,840,141 | A→G | intergenic (‑148/‑74) | nlpA ← / → yicS | lipoprotein‑28/uncharacterized protein YicS |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,892,750 | G→A | R379H (CGC→CAC) | mdtL → | efflux pump MdtL |
| RA | 3,930,797 | A→G | R99R (CGT→CGC) | ravA ← | regulatory ATPase RavA |
| RA | 3,939,346 | T→C | T423A (ACA→GCA) | hsrA ← | putative transporter HsrA |
| RA | 4,012,247 | T→C | L190L (TTA→TTG) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,052,658 | C→T | S205F (TCC→TTC) | hemN → | coproporphyrinogen III dehydrogenase |
| RA | 4,085,641 | A→G | M61T (ATG→ACG) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,093,410 | A→G | V10A (GTA→GCA) | rhaM ← | L‑rhamnose mutarotase |
| RA | 4,109,766 | A→G | K311K (AAA→AAG) | sbp → | sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp |
| RA | 4,226,250 | C→T | T808M (ACG→ATG) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,242,009 | G→A | F82F (TTC→TTT) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,293,106 | (G)7→8 | coding (1595/1659 nt) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,297,147 | G→A | intergenic (‑22/+72) | yjcO ← / ← fdhF | Sel1 repeat‑containing protein YjcO/formate dehydrogenase H |
| RA | 4,337,675 | C→T | T85T (ACG→ACA) | adiY ← | DNA‑binding transcriptional activator AdiY |
| RA | 4,375,356 | A→G | V101A (GTG→GCG) | epmB ← | lysine 2,3‑aminomutase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,478,011 | A→G | Y101H (TAT→CAT) | argI ← | ornithine carbamoyltransferase ArgI |
| RA | 4,478,943 | C→T | intergenic (+54/+91) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,519,446 | T→C | E293E (GAA→GAG) | yjhU ← | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU |
| RA | 4,536,360 | A→G | intergenic (+329/+254) | yjhR → / ← nanS | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR/N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,547,354 | T→C | Y753Y (TAT→TAC) | fimD → | type I fimbriae usher protein |
| RA | 4,579,424 | T→C | intergenic (‑87/+75) | mcrB ← / ← symE | 5‑methylcytosine‑specific restriction enzyme subunit McrB/toxic protein SymE |
| RA | 4,640,270 | A→G | L13L (TTG→CTG) | arcA ← | DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1532115–1532162 | 1532814–1532688 | 527–700 | 18 [16] | [16] 17 | ydcC | H repeat‑associated putative transposase YdcC |
| * | * | ÷ | NC_000913 | 2066289–2066464 | 2066606–2066466 | 3–318 | 18 [16] | [16] 18 | [insH‑6] | [insH‑6] |
| * | * | ÷ | NC_000913 | 3423778–3424234 | 3424525–3424241 | 8–748 | 17 [16] | [10] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 99 (1.430) | 17 (0.280) | 14/244 | 2.6 | 20.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 47 (0.770) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 78 (1.160) | 56/268 | 0.1 | 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 = | 92 (1.330) | 88 (1.280) | 49/274 | 0.2 | 65.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 61 (0.880) | 49/276 | 0.2 | 98.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.010) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||