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 |
| RA | 138,793 | C→A | intergenic (+160/+42) | cueO → / ← gcd | cuprous oxidase/multicopper oxidase with role in copper homeostasis/quinoprotein glucose dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 283,803 | G→T | V201V (GTG→GTT) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 361,130 | G→T | W380L (TGG→TTG) | cynX → | cyanate transporter |
| RA | 447,009 | A→T | Y233N (TAT→AAT) | cyoE ← | heme O synthase |
| RA | 547,658 | C→A | P327T (CCT→ACT) | fdrA → | putative acyl‑CoA synthetase FdrA |
| RA | 574,267 | C→A | G104G (GGC→GGA) | ybcQ → | DLP12 prophage; putative antitermination protein |
| RA | 598,114 | G→T | A212A (GCG→GCT) | cusB → | copper/silver export system membrane fusion protein |
| RA | 632,683 | C→A | V265V (GTG→GTT) | hcxA ← | hydroxycarboxylate dehydrogenase A |
| RA | 765,914 | C→A | intergenic (‑39/‑70) | mngR ← / → mngA | DNA‑binding transcriptional repressor MngR/2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 898,314 | G→C | W109S (TGG→TCG) | ybjO → | putative inner membrane protein |
| RA | 979,123 | C→A | P933Q (CCG→CAG) | mukB → | chromosome partitioning protein MukB |
| RA | 1,072,489 | C→A | Q125H (CAG→CAT) | rutB ← | peroxyureidoacrylate/ureidoacrylate amidohydrolase |
| RA | 1,120,278 | G→A | V103V (GTC→GTT) | solA ← | N‑methyl‑L‑tryptophan oxidase |
| RA | 1,265,001 | C→A | intergenic (+31/‑11) | hemA → / → prfA | glutamyl‑tRNA reductase/peptide chain release factor RF1 |
| RA | 1,304,457 | C→A | G208G (GGC→GGA) | oppC → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppC |
| RA | 1,678,134 | G→T | intergenic (‑231/‑293) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase subunit alpha/DUF1471 domain‑containing protein YdgH |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,750,451 | G→T | A188E (GCG→GAG) | ydhX ← | putative 4Fe‑4S ferredoxin‑type protein |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,909,685 | G→T | R139S (CGT→AGT) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 1,954,643 | T→C | I789V (ATC→GTC) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,955,924 | C→A | E362* (GAA→TAA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,057,292 | C→A | D145E (GAC→GAA) | yeeN → | putative transcriptional regulator YeeN |
| RA | 2,074,054 | G→T | W839L (TGG→TTG) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,213,853 | G→C | D264E (GAC→GAG) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,299,622 | C→A | G213G (GGG→GGT) | napG ← | ferredoxin‑type protein NapG |
| RA | 2,506,758 | C→A | L379L (CTG→CTT) | fryC ← | putative PTS enzyme IIC component FryC |
| RA | 2,617,540 | C→A | P483T (CCT→ACT) | bepA → | beta‑barrel assembly‑enhancing protease |
| RA | 2,656,493 | G→T | intergenic (‑135/+43) | pepB ← / ← iscX | aminopeptidase B/accessory iron‑sulfur cluster assembly protein IscX |
| RA | 2,769,287 | G→A | R208H (CGC→CAC) | yfjQ → | CP4‑57 prophage; protein YfjQ |
| RA | 2,770,129 | C→A | L143M (CTG→ATG) | yfjR → | CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,833,602 | G→T | R376L (CGA→CTA) | norV → | anaerobic nitric oxide reductase flavorubredoxin |
| RA | 2,835,672 | C→A | G585V (GGA→GTA) | hypF ← | carbamoyltransferase HypF |
| RA | 3,153,929 | C→A | L123M (CTG→ATG) | yghB → | DedA family protein YghB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,395,064 | C→A | D399Y (GAT→TAT) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,132 | C→A | V484L (GTG→TTG) | glgP ← | glycogen phosphorylase |
| RA | 3,656,343 | C→A | intergenic (‑51/+65) | hdeB ← / ← hdeA | periplasmic acid stress chaperone/HdeA monomer, chaperone active form |
| RA | 3,675,798 | C→A | P338Q (CCA→CAA) | yhjE → | putative transporter YhjE |
| RA | 3,705,758 | G→T | L11L (CTC→CTA) | dppB ← | dipeptide ABC transporter membrane subunit DppB |
| RA | 3,740,617 | G→T | V305F (GTC→TTC) | avtA → | valine‑‑pyruvate aminotransferase |
| RA | 3,754,000 | G→T | L34M (CTG→ATG) | yiaV ← | putative membrane fusion protein |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,840,746 | G→T | R332S (CGC→AGC) | nepI ← | purine ribonucleoside exporter |
| RA | 4,142,527 | C→A | intergenic (‑306/‑3) | ptsA ← / → frwC | putative PTS multiphosphoryl transfer protein PtsA/putative PTS enzyme IIC component FrwC |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,294,762 | C→A | V94V (GTC→GTA) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,332,509 | C→A | R255L (CGG→CTG) | basS ← | sensory histidine kinase BasS |
| RA | 4,347,593 | C→G | P384P (CCG→CCC) | dcuB ← | anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,445,749 | G→T | A546A (GCG→GCT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,493,330 | C→A | A8S (GCA→TCA) | idnO ← | 5‑keto‑D‑gluconate 5‑reductase |
| RA | 4,565,819 | A→T | F11Y (TTC→TAC) | yjiM ← | putative dehydratase subunit |
| RA | 4,569,073 | G→T | pseudogene (76/921 nt) | rpnD → | truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,571,333 | G→A | P81L (CCG→CTG) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,591,735 | G→T | G27C (GGT→TGT) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102983 | 3104082 | 1100 | 19 [18] | [18] 20 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423761–3424234 | 3424525–3424239 | 6–765 | 20 [17] | [16] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 19 (0.250) | 85 (1.240) | 51/246 | 0.1 | 82.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 20 (0.290) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 19 (0.250) | 64 (0.930) | 49/246 | 0.1 | 77.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 20 (0.290) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 107 (1.420) | 61/270 | 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 = | 142 (1.830) | 119 (1.550) | 57/276 | 0.1 | 62.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 75 (0.970) | 41/278 | 0.5 | 93.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||