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 | 127,167 | G→T | K491N (AAG→AAT) | aceF → | pyruvate dehydrogenase, E2 subunit |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 312,789 | G→A | intergenic (‑12/+352) | ykgM ← / ← ykgR | putative ribosomal protein/putative membrane protein YkgR |
| RA | 434,100 | C→A | Q216K (CAG→AAG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 524,094 | C→A | F278L (TTC→TTA) | rhsD → | protein RhsD |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 979,183 | C→A | A953D (GCC→GAC) | mukB → | chromosome partitioning protein MukB |
| RA | 1,075,591 | G→T | P1098T (CCG→ACG) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,181,365 | C→A | G121W (GGG→TGG) | ymfA ← | putative inner membrane protein |
| RA | 1,260,443 | G→T | L121M (CTG→ATG) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | 1,305,652 | C→A | P300Q (CCG→CAG) | oppD → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppD |
| RA | 1,467,182 | G→T | pseudogene (1791/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,575,419 | C→A | W734L (TGG→TTG) | yddB ← | putative TonB‑dependent receptor |
| JC JC | 1,623,963 | IS1 (+) +9 bp | intergenic (‑113/+134) | dgcZ ← / ← ydeI | diguanylate cyclase DgcZ/BOF family protein YdeI |
| RA | 1,642,413 | G→T | intergenic (+202/+76) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,725,682 | C→A | *80L (TGA→TTA) | ydhL ← | conserved protein YdhL |
| RA | 1,859,965 | T→C | N89D (AAT→GAT) | ydjK ← | putative transporter YdjK |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,025,858 | G→T | T116T (ACG→ACT) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,168,867 | G→T | E52D (GAG→GAT) | yegS → | lipid kinase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC JC | 2,273,195 | IS1 (+) +8 bp | coding (832‑839/1815 nt) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,403,820 | G→T | P9H (CCC→CAC) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,414,112 | G→T | G215C (GGT→TGT) | ackA → | acetate kinase |
| RA | 2,566,086 | C→A | E267* (GAA→TAA) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,569,681 | C→A | G219G (GGG→GGT) | eutJ ← | putative chaperonin, ethanolamine utilization protein |
| RA | 2,578,259 | G→T | S40* (TCA→TAA) | maeB ← | malate dehydrogenase |
| RA | 2,602,199 | C→A | L128M (CTG→ATG) | hyfB → | hydrogenase 4 component B |
| RA | 2,610,050 | G→T | D522Y (GAC→TAC) | hyfG → | hydrogenase 4 catalytic subunit HyfG |
| RA | 2,818,989 | G→T | A53D (GCT→GAT) | csrA ← | carbon storage regulator |
| RA | 2,831,224 | G→T | P356T (CCG→ACG) | norR ← | DNA‑binding transcriptional dual regulator NorR |
| RA | 2,940,438 | C→A | S269I (AGC→ATC) | rlmM ← | 23S rRNA 2'‑O‑ribose C2498 methyltransferase |
| RA | 3,002,178 | C→A | L612M (CTG→ATG) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,121,435 | G→T | intergenic (‑156/+199) | glcA ← / ← glcB | glycolate/lactate:H(+) symporter GlcA/malate synthase G |
| RA | 3,203,636 | G→T | L166M (CTG→ATG) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,242,301 | C→A | P338P (CCG→CCT) | uxaA ← | D‑altronate dehydratase |
| RA | 3,247,284 | G→T | K211N (AAG→AAT) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,410,940 | C→A | L221M (CTG→ATG) | dusB → | tRNA‑dihydrouridine synthase B |
| 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 |
| RA | 3,833,060 | C→A | S493I (AGC→ATC) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,891,534 | C→T | intergenic (+51/‑81) | tnaB → / → mdtL | tryptophan:H(+) symporter TnaB/efflux pump MdtL |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,287,594 | C→A | intergenic (‑223/‑170) | acs ← / → nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,319,756 | G→T | A303E (GCG→GAG) | phnI ← | carbon‑phosphorus lyase core complex subunit PhnI |
| RA | 4,412,487 | G→T | R34L (CGC→CTC) | yjfM → | DUF1190 domain‑containing protein YjfM |
| RA | 4,440,035 | G→T | P394Q (CCG→CAG) | ytfL ← | putative inner membrane protein |
| RA | 4,500,309 | C→A | pseudogene (483/1199 nt) | yjgX ← | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment |
| RA | 4,617,038 | G→T | Q10K (CAA→AAA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| RA | 4,625,193 | C→A | P100Q (CCG→CAG) | serB → | phosphoserine phosphatase |
| RA | 4,639,167 | G→T | G330G (GGG→GGT) | creD → | putative inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102973 | 3104052 | 1080 | 40 [38] | [37] 40 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423761–3424234 | 3424531–3424238 | 5–771 | 40 [38] | [37] 39 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 30 (0.230) | 177 (1.520) | 72/246 | 0.1 | 89.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 14 (0.120) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.230) | 131 (1.120) | 60/246 | 0.3 | 86.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 14 (0.120) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 168 (1.310) | 85/270 | 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 = | 225 (1.710) | 181 (1.380) | 81/276 | 0.1 | 61.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 118 (0.900) | 62/278 | 0.5 | 92.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||