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 | 111,016 | T→C | 8.3% | intergenic (+32/‑28) | secA → / → mutT | protein translocation ATPase/8‑oxo‑dGTP diphosphatase |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 672,110 | G→A | 8.2% | T26I (ACC→ATC) | lptE ← | lipopolysaccharide assembly protein LptE |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 1,048,429 | C→T | 8.2% | W88* (TGG→TAG) ‡ | gfcC ← | capsule biosynthesis GfcC family protein |
| RA | 1,048,430 | A→G | 10.0% | W88R (TGG→CGG) ‡ | gfcC ← | capsule biosynthesis GfcC family protein |
| RA | 1,151,874 | T→A | 9.1% | intergenic (+23/‑65) | acpP → / → fabF | acyl carrier protein/beta‑ketoacyl‑[acyl carrier protein] synthase II |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,309,640 | A→G | 12.7% | I210I (ATT→ATC) | kch ← | K(+) channel Kch |
| RA | 1,971,929 | A→C | 9.4% | S255A (TCA→GCA) | tar ← | methyl‑accepting chemotaxis protein Tar |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,581,765 | T→C | 6.8% | D338G (GAC→GGC) | ypfG ← | DUF1176 domain‑containing protein YpfG |
| RA | 2,632,586 | G→C | 6.3% | intergenic (‑51/+18) | guaA ← / ← guaB | GMP synthetase/inosine 5'‑monophosphate dehydrogenase |
| RA | 2,632,588 | A→T | 6.4% | intergenic (‑53/+16) | guaA ← / ← guaB | GMP synthetase/inosine 5'‑monophosphate dehydrogenase |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,778,123 | G→T | 9.3% | intergenic (+341/+23) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,800,517 | T→A | 11.8% | intergenic (+42/‑206) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 2,800,519 | T→G | 7.8% | intergenic (+44/‑204) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 2,866,487 | G→C | 7.0% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter YgbN/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,866,488 | G→C | 7.0% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter YgbN/RNA polymerase, sigma S (sigma 38) factor |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,156,590 | C→A | 9.3% | intergenic (+72/‑33) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,156,591 | T→G | 9.1% | intergenic (+73/‑32) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,276,891 | T→G | 8.2% | intergenic (+38/‑111) | garD → / → prlF | galactarate dehydratase/antitoxin PrlF |
| RA | 3,309,004 | C→T | 5.9% | intergenic (‑80/+29) | nlpI ← / ← pnp | lipoprotein NlpI/polynucleotide phosphorylase |
| RA | 3,309,009 | C→T | 5.8% | intergenic (‑85/+24) | nlpI ← / ← pnp | lipoprotein NlpI/polynucleotide phosphorylase |
| RA | 3,309,012 | A→G | 5.9% | intergenic (‑88/+21) | nlpI ← / ← pnp | lipoprotein NlpI/polynucleotide phosphorylase |
| RA | 3,332,822 | G→A | 11.2% | intergenic (‑87/+40) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,332,823 | T→C | 13.4% | intergenic (‑88/+39) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,439,588 | G→C | 7.9% | intergenic (‑79/+28) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 7.5% | intergenic (‑80/+27) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,774,207 | C→T | 9.0% | intergenic (+13/‑217) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,774,214 | C→T | 11.5% | intergenic (+20/‑210) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,774,215 | A→G | 11.1% | intergenic (+21/‑209) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,774,222 | A→G | 11.7% | intergenic (+28/‑202) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,911,819 | T→G | 9.1% | intergenic (‑294/+20) | pstS ← / ← glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,923,417 | A→G | 7.4% | P88P (CCT→CCC) | rsmG ← | 16S rRNA m(7)G527 methyltransferase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,138,006 | T→G | 10.0% | T344P (ACG→CCG) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,138,011 | C→A | 10.2% | G342V (GGC→GTC) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,177,171 | T→A | 10.2% | intergenic (+43/‑187) | tufB → / → secE | translation elongation factor Tu 2/Sec translocon subunit SecE |
| RA | 4,177,172 | T→A | 9.1% | intergenic (+44/‑186) | tufB → / → secE | translation elongation factor Tu 2/Sec translocon subunit SecE |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 25.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,496,511 | A→G | 7.2% | intergenic (+22/‑239) | leuX → / → intB | tRNA‑Leu/KpLE2 phage‑like element; putative integrase |
| RA | 4,496,512 | C→T | 6.2% | intergenic (+23/‑238) | leuX → / → intB | tRNA‑Leu/KpLE2 phage‑like element; putative integrase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423731–3424234 | 3424531–3424238 | 5–801 | 18 [17] | [17] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 315563 = | NA (NA) | 3 (0.070) | 3/244 | NT | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 9 (0.210) | 6/244 | NT | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315843 = | NA (NA) | 9 (0.200) | 7/258 | NT | NA | noncoding (615/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315886 = | NA (NA) | noncoding (658/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315852 | NA (NA) | 21 (0.460) | 6/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 484065 = | 50 (1.070) | 3 (0.070) | 3/258 | NT | 5.7% | coding (339/3150 nt) | acrB | multidrug efflux pump RND permease AcrB |
| ? | NC_000913 | 484089 = | 51 (1.120) | coding (315/3150 nt) | acrB | multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2171 (46.830) | 257/262 | NT | 98.1% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 43 (0.920) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 566841 | 28 (0.600) | 8 (0.230) +34 bp |
5/196 | NT | 23.3% | noncoding (65/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 43 (0.920) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 983123 = | 36 (0.770) | 3 (0.070) | 3/252 | NT | 8.5% | coding (49/549 nt) | ycbK | DUF882 domain‑containing protein YcbK |
| ? | NC_000913 | 983167 = | 30 (0.670) | coding (93/549 nt) | ycbK | DUF882 domain‑containing protein YcbK | |||||
| * | ? | NC_000913 | 1207790 = | 10 (0.210) | 16 (0.390) | 15/232 | NT | 56.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 16 (0.390) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.260) | 14 (0.340) | 13/232 | NT | 51.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.390) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 56 (1.240) | 47/256 | NT | 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 | 1417458 = | 42 (0.900) | 3 (0.070) | 3/244 | NT | 7.5% | intergenic (‑72/+30) | recE/racC | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific/Rac prophage; protein RacC |
| ? | NC_000913 | 1417483 = | 35 (0.810) | intergenic (‑97/+5) | recE/racC | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific/Rac prophage; protein RacC | |||||
| * | ? | NC_000913 | = 1451535 | 53 (1.130) | 3 (0.070) | 3/252 | NT | 5.6% | intergenic (‑186/+62) | tynA/paaZ | copper‑containing amine oxidase/oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| ? | NC_000913 | = 1451538 | 50 (1.120) | intergenic (‑189/+59) | tynA/paaZ | copper‑containing amine oxidase/oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase | |||||
| * | ? | NC_000913 | = 1460521 | 53 (1.130) | 4 (0.090) | 4/250 | NT | 7.3% | coding (51/423 nt) | paaI | phenylacetyl‑CoA thioesterase |
| ? | NC_000913 | = 1460536 | 52 (1.180) | coding (66/423 nt) | paaI | phenylacetyl‑CoA thioesterase | |||||
| * | ? | NC_000913 | = 1879834 | 42 (0.920) | 3 (0.070) | 3/258 | NT | 6.7% | coding (115/360 nt) | yeaR | DUF1971 domain‑containing protein YeaR |
| ? | NC_000913 | = 2515616 | NA (NA) | noncoding (1344/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 1886815 = | 43 (0.920) | 3 (0.070) | 3/242 | NT | 8.2% | intergenic (+5/+49) | yeaX/rnd | carnitine monooxygenase subunit YeaX/RNase D |
| ? | NC_000913 | 1886858 = | 28 (0.650) | intergenic (+48/+6) | yeaX/rnd | carnitine monooxygenase subunit YeaX/RNase D | |||||
| * | ? | NC_000913 | = 2191628 | 45 (0.960) | 3 (0.070) | 3/252 | NT | 6.5% | coding (18/720 nt) | yehC | putative fimbrial chaperone YehC |
| ? | NC_000913 | = 2191637 | 43 (0.960) | coding (9/720 nt) | yehC | putative fimbrial chaperone YehC | |||||
| * | ? | NC_000913 | = 2347432 | 56 (1.200) | 3 (0.070) | 3/248 | NT | 5.3% | coding (49/1131 nt) | nrdB | ribonucleoside‑diphosphate reductase 1 subunit beta |
| ? | NC_000913 | = 2347436 | 54 (1.230) | coding (53/1131 nt) | nrdB | ribonucleoside‑diphosphate reductase 1 subunit beta | |||||
| * | ? | NC_000913 | 2726026 = | 52 (1.110) | 3 (0.060) +A |
3/262 | NT | 5.3% | intergenic (‑280/+43) | kgtP/rrfG | alpha‑ketoglutarate:H(+) symporter/5S ribosomal RNA |
| ? | NC_000913 | = 4171761 | 57 (1.220) | intergenic (+5/‑296) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 5 (0.110) | 5/252 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3741088 | NA (NA) | 3 (0.070) | 3/244 | NT | NA | intergenic (+130/+21) | avtA/ysaA | valine‑‑pyruvate aminotransferase/putative electron transport protein YsaA |
| ? | NC_000913 | = 3741092 | NA (NA) | intergenic (+134/+17) | avtA/ysaA | valine‑‑pyruvate aminotransferase/putative electron transport protein YsaA | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 4 (0.090) | 4/250 | NT | 15.0% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA |
| ? | NC_000913 | = 3943642 | 24 (0.510) | intergenic (+132/‑62) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 4171625 | 36 (0.770) | 4 (0.090) | 3/252 | NT | 10.4% | intergenic (+81/‑12) | rrlB/rrfB | 23S ribosomal RNA/5S ribosomal RNA |
| ? | NC_000913 | = 4213004 | NA (NA) | intergenic (+58/‑36) | rrlE/rrfE | 23S ribosomal RNA/5S ribosomal RNA | |||||
| * | ? | NC_000913 | 4542682 = | 36 (0.770) | 14 (0.320) | 14/246 | NT | 28.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 37 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 36 (0.770) | 13 (0.300) | 13/246 | NT | 26.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 37 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4576863 = | 53 (1.130) | 3 (0.070) | 3/244 | NT | 5.8% | intergenic (+8/+49) | yjiV/mcrC | putative uncharacterized protein YjiV/5‑methylcytosine‑specific restriction enzyme subunit McrC |
| ? | NC_000913 | 4576890 = | 48 (1.110) | intergenic (+35/+22) | yjiV/mcrC | putative uncharacterized protein YjiV/5‑methylcytosine‑specific restriction enzyme subunit McrC | |||||
| * | ? | NC_000913 | 4628744 = | NA (NA) | 3 (0.070) | 3/250 | NT | NA | noncoding (1/37 nt) | other | REP354b |
| ? | NC_000913 | 4628775 = | NA (NA) | noncoding (32/37 nt) | other | REP354b | |||||