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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,020,961 | A→G | intergenic (‑42/‑177) | sulA ← / → sxy | cell division inhibitor SulA/transcriptional coactivator for CRP |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,600,426 | C→T | A272A (GCG→GCA) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,647,030 | C→T | intergenic (+293/+144) | flxA → / ← ydfW | Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,953,436 | Δ1 bp | coding (735/744 nt) | cmoA → | carboxy‑S‑adenosyl‑L‑methionine synthase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,618,360 | T→C | P139P (CCA→CCG) | hda ← | inibitor of reinitiation of DNA replication |
| RA | 2,798,780 | A→G | intergenic (‑285/‑384) | stpA ← / → alaE | DNA‑binding transcriptional repressor StpA with RNA chaperone activity/L‑alanine exporter |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| MC JC | 4,142,990 | Δ235 bp | coding (461‑695/1080 nt) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,267,869 | C→T | Y252Y (TAC→TAT) | tyrB → | tyrosine aminotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,462,837 | T→C | intergenic (‑177/+217) | nrdD ← / ← treC | anaerobic ribonucleoside‑triphosphate reductase/trehalose‑6‑phosphate hydrolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196304 | 1211419 | 15116 | 4 [2] | [3] 4 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 1437231 | 1437359 | 129 | 4 [3] | [3] 4 | [ydbK] | [ydbK] |
| * | * | ÷ | NC_000913 | 1438142 | 1438429 | 288 | 4 [3] | [2] 4 | ydbK | putative pyruvate‑flavodoxin oxidoreductase |
| * | * | ÷ | NC_000913 | 1440210 | 1440395 | 186 | 4 [3] | [3] 4 | ydbK | putative pyruvate‑flavodoxin oxidoreductase |
| * | * | ÷ | NC_000913 | 1440515 | 1440713 | 199 | 4 [3] | [2] 4 | ydbK | putative pyruvate‑flavodoxin oxidoreductase |
| * | * | ÷ | NC_000913 | 1441040 | 1441328 | 289 | 4 [3] | [3] 4 | ydbJ–[hslJ] | ydbJ,[hslJ] |
| * | * | ÷ | NC_000913 | 1441600 | 1441778 | 179 | 4 [3] | [2] 4 | [hslJ] | [hslJ] |
| * | * | ÷ | NC_000913 | 1442562 | 1442816 | 255 | 4 [3] | [3] 4 | ldhA | D‑lactate dehydrogenase |
| * | * | ÷ | NC_000913 | 1444109 | 1444328 | 220 | 4 [3] | [3] 4 | ydbH | PF11739 family protein YdbH |
| * | * | ÷ | NC_000913 | 1447963 | 1448270 | 308 | 4 [1] | [3] 4 | feaB | phenylacetaldehyde dehydrogenase |
| * | * | ÷ | NC_000913 | 1454172 | 1454547 | 376 | 5 [2] | [3] 4 | paaA | phenylacetyl‑CoA 1,2‑epoxidase, monooxygenase subunit |
| * | * | ÷ | NC_000913 | 1455845 | 1456040 | 196 | 4 [3] | [3] 5 | [paaC]–[paaD] | [paaC],[paaD] |
| * | * | ÷ | NC_000913 | 1458328 | 1458620 | 293 | 4 [2] | [3] 4 | paaG | putative ring 1,2‑epoxyphenylacetyl‑CoA isomerase (oxepin‑CoA forming) |
| * | * | ÷ | NC_000913 | 1458806 | 1459654 | 849 | 4 [3] | [3] 4 | [paaG]–[paaH] | [paaG],[paaH] |
| * | * | ÷ | NC_000913 | 1461489 | 1461573 | 85 | 4 [3] | [3] 4 | paaJ | beta‑ketoadipyl‑CoA thiolase |
| * | * | ÷ | NC_000913 | 1467971–1469238 | 1590764 | 121527–122794 | 5 [3] | [0] 1280 | [insD‑2]–yneL | [insD‑2],insC‑2,ydbA,insI‑2,ydbA,pdxI,ydbD,ynbA,ynbB,ynbC,ynbD,azoR,hrpA,ydcF,aldA,gapC,cybB,rydC,ydcA,hokB,mokB,sokB,trg,ydcI,ydcJ,opgD,ydcH,rimL,ydcK,tehA,tehB,ydcL,insQ,ydcO,sutR,rlhA,yncJ,hicA,hicB,ydcR,ydcS,ydcT,ydcU,ydcV,patD,yncL,ortT,ydcY,ydcZ,mnaT,curA,mcbR,yncD,yncE,ansP,yncG,yncH,rhsE,ydcD,yncO,yncI,ydcC,pptA,yddH,nhoA,yddE,narV,narW,narY,narZ,narU,yddJ,yddK,yddL,yddG,fdnG,fdnH,fdnI,yddM,adhP,maeA,sra,bdm,osmC,ddpF,ddpD,ddpC,ddpB,ddpA,ddpX,dosP,dosC,yddY,yddW,gadC,gadB,pqqL,yddB,yddA,yneP,ydeM,ydeN,ydeO,safA,ydeP,ydeQ,ydeR,ydeS,ydeT,yneL |
| * | * | ÷ | NC_000913 | 3423795–3424230 | 3424523–3424238 | 9–729 | 4 [3] | [3] 4 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3751949 | 3751971 | 23 | 4 [3] | [2] 4 | yiaT/yiaU | outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1432951 | NA (NA) | 7 (0.170) | 7/276 | 1.8 | NA | coding (541/576 nt) | tfaR | Rac prophage; putative tail fiber assembly protein TfaR |
| ? | NC_000913 | = 1433168 | NA (NA) | coding (507/591 nt) | pinR | Rac prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | 1590765 = | 0 (0.000) | 1257 (32.560) | 178/266 | 0.0 | 99.4% | intergenic (‑229/+89) | yneL/hipA | putative HTH‑type transcriptional regulator YneL/serine/threonine kinase HipA |
| ? | NC_000913 | = 1647024 | 15 (0.390) | intergenic (+287/+150) | flxA/ydfW | Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW | |||||
| * | ? | NC_000913 | 3363001 = | 40 (1.000) | 34 (0.850) | 25/274 | 0.2 | 62.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 34 (0.850) | 27/276 | 0.1 | 87.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.120) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||