mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 33,170 | Δ1 bp | 11.8% | coding (2354/3222 nt) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 402,427 | C→T | 16.3% | G227G (GGC→GGT) | phoA → | alkaline phosphatase |
| RA | 460,772 | T→G | 100% | S629A (TCG→GCG) | lon → | Lon protease |
| RA | 694,189 | G→A | 12.0% | P256L (CCG→CTG) | miaB ← | isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 802,778 | G→T | 48.4% | V298L (GTG→TTG) | ybhI → | putative tricarboxylate transporter |
| RA | 921,997 | C→T | 16.0% | R551W (CGG→TGG) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,440,789 | C→A | 24.9% | intergenic (‑5/‑269) | ydbK ← / → ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ |
| RA | 1,852,271 | C→T | 100% | R129C (CGG→TGC) | pncA → | nicotinamidase |
| RA | 1,852,273 | G→C | 100% | R129C (CGG→TGC) | pncA → | nicotinamidase |
| RA | 1,934,844 | C→A | 100% | E491* (GAG→TAG) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| 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 | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,414,002 | G→A | 12.0% | R178H (CGT→CAT) | ackA → | acetate kinase |
| RA | 2,525,908 | C→G | 20.1% | intergenic (+17/+22) | yfeN → / ← yfeR | conserved outer membrane protein YfeN/putative LysR‑type DNA‑binding transcriptional regulator YfeR |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,667,575 | G→A | 17.5% | A91V (GCG→GTG) | hcaT ← | putative 3‑phenylpropionate transporter |
| RA | 2,818,393 | A→T | 11.2% | intergenic (‑119/+80) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,101,655 | T→A | 11.8% | intergenic (‑32/+152) | yggN ← / ← yggL | putative EcfF/protein YggL |
| RA | 3,101,656 | T→A | 11.8% | intergenic (‑33/+151) | yggN ← / ← yggL | putative EcfF/protein YggL |
| RA | 3,148,446 | G→A | 13.1% | E184K (GAG→AAG) | gpr → | L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,407,293 | T→A | 9.0% | intergenic (+27/‑82) | accC → / → yhdT | biotin carboxylase/DUF997 domain‑containing protein YhdT |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,898,291 | C→A | 12.2% | D90E (GAC→GAA) | cbrC → | UPF0167 family colicin E2 tolerance protein CbrC |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,034,547 | A→G | 100% | E468G (GAG→GGG) | trkH → | K(+) transporter TrkH |
| RA | 4,051,262 | A→C | 8.5% | noncoding (227/245 nt) | csrC → | small regulatory RNA CsrC |
| RA | 4,183,275 | C→G | 100% | N677K (AAC→AAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,204 | G→A | 100% | intergenic (‑105/+128) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 32.6% | 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 | 4,362,529 | T→C | 11.5% | intergenic (‑595/+22) | cadC ← / ← pheU | DNA‑binding transcriptional activator CadC/tRNA‑Phe |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366063 | 366418 | 356 | 9 [8] | [8] 9 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913 | 3423759–3424233 | 3424520–3424238 | 6–762 | 10 [8] | [8] 10 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315572 | NA (NA) | 7 (0.260) | 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 | = 315852 | NA (NA) | 23 (0.810) | 15/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316093 | NA (NA) | 8 (0.280) | 6/258 | NT | NA | noncoding (865/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316135 | NA (NA) | noncoding (907/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392478 = | NA (NA) | 8 (0.280) | 4/260 | NT | NA | noncoding (489/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392552 = | NA (NA) | noncoding (415/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1778 (61.240) | 255/262 | NT | 98.5% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 27 (0.920) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 27 (0.920) | 4 (0.180) +34 bp |
3/196 | NT | 24.1% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 7 (0.240) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 608008 = | NA (NA) | 7 (0.240) | 7/258 | NT | 18.9% | noncoding (2/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 839235 | 30 (1.050) | intergenic (‑28/+14) | ybiX/fiu | PKHD‑type hydroxylase YbiX/putative iron siderophore outer membrane transporter | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.510) | 11 (0.430) | 11/232 | NT | 44.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 14 (0.550) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.550) | 8 (0.310) | 7/232 | NT | 36.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 14 (0.550) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1427774 = | 29 (0.990) | 8 (0.270) | 7/264 | NT | 22.5% | noncoding (1021/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1440910 | 26 (0.890) | intergenic (‑126/‑148) | ydbK/ydbJ | putative pyruvate‑flavodoxin oxidoreductase/DUF333 domain‑containing protein YdbJ | |||||
| * | ? | NC_000913 | 3540274 = | 26 (0.890) | 3 (0.110) | 3/256 | NT | 11.1% | coding (112/228 nt) | feoA | ferrous iron transport protein A |
| ? | NC_000913 | 3540310 = | 23 (0.810) | coding (148/228 nt) | feoA | ferrous iron transport protein A | |||||
| * | ? | NC_000913 | = 3944652 | NA (NA) | 3 (0.110) | 3/256 | NT | NA | noncoding (949/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | = 3944670 | NA (NA) | noncoding (967/2904 nt) | rrlC | 23S ribosomal RNA | |||||