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 | 11,843 | A→G | intergenic (‑57/‑320) | yaaI ← / → dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| RA | 162,800 | G→T | L232L (CTG→CTT) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 216,895 | C→A | A37S (GCC→TCC) | yaeF ← | peptidase C92 family protein |
| RA | 248,885 | C→A | pseudogene (1186/1713 nt) | lfhA ← | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 260,977 | C→A | A197E (GCA→GAA) | proB → | glutamate 5‑kinase |
| RA | 273,037 | G→T | R64I (AGA→ATA) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 345,634 | C→G | I77M (ATC→ATG) | yahM → | uncharacterized protein YahM |
| RA | 438,373 | G→T | A602D (GCC→GAC) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 657,527 | C→A | intergenic (+26/+28) | cspE → / ← crcB | transcription antiterminator and regulator of RNA stability/F(‑) channel |
| RA | 730,713 | T→C | S377S (AGT→AGC) | rhsC → | rhs element protein RhsC |
| RA | 743,686 | C→A | R32R (CGA→AGA) | pxpB → | 5‑oxoprolinase component B |
| RA | 781,266 | G→T | intergenic (+44/‑103) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 804,254 | G→T | S251I (AGT→ATT) | ybhJ → | putative hydratase YbhJ |
| RA | 863,883 | A→G | D81G (GAT→GGT) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,232,026 | G→T | E281* (GAG→TAG) | umuC → | DNA polymerase V catalytic protein |
| RA | 1,241,617 | G→T | S152* (TCG→TAG) | cvrA ← | putative K(+):H(+) antiporter |
| RA | 1,270,590 | A→G | intergenic (+130/+159) | rdlC → / ← chaA | small regulatory antisense RNA RdlC/Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,461,985 | C→A | R365S (CGC→AGC) | paaJ → | beta‑ketoadipyl‑CoA thiolase |
| RA | 1,525,848 | C→A | G45C (GGC→TGC) | ansP ← | L‑asparagine transporter |
| RA | 1,531,968 | G→A | G51G (GGG→GGA) | ydcC → | H repeat‑associated putative transposase YdcC |
| RA | 1,672,355 | G→T | G132G (GGG→GGT) | ydgD → | putative serine protease YdgD |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,772,181 | Δ1 bp | coding (1111/1215 nt) | ydiM → | putative exporter YdiM |
| RA | 1,849,590 | G→T | E252* (GAG→TAG) | sppA → | protease IV, a signal peptide peptidase |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,908,123 | T→C | intergenic (‑532/+138) | yobF ← / ← yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,112,528 | G→T | V178V (GTC→GTA) | rfbB ← | dTDP‑glucose 4,6‑dehydratase 1 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,264,955 | G→T | E365* (GAG→TAG) | setB → | sugar exporter SetB |
| RA | 2,456,005 | G→T | intergenic (‑359/+322) | yfcV ← / ← sixA | putative fimbrial protein YfcV/phosphohistidine phosphatase |
| RA | 2,501,727 | C→A | R200S (CGC→AGC) | ypdC → | putative AraC‑type DNA‑binding transcriptional regulator YpdC |
| RA | 2,541,193 | G→T | R163S (CGC→AGC) | cysW ← | sulfate/thiosulfate ABC transporter inner membrane subunit CysW |
| RA | 2,564,803 | C→A | P94Q (CCG→CAG) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,566,516 | C→A | G123G (GGG→GGT) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,735,495 | C→A | A173S (GCG→TCG) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase |
| RA | 2,829,646 | C→A | R200R (CGC→CGA) | srlR → | DNA‑binding transcriptional repressor SrlR |
| RA | 2,994,412 | C→A | pseudogene (474/503 nt) | pbl → | transglycosylase domain‑containing protein Pbl |
| RA | 3,036,812 | G→T | A432E (GCG→GAG) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,176,911 | C→A | D124Y (GAC→TAC) | yqiB ← | DUF1249 domain‑containing protein YqiB |
| RA | 3,279,496 | G→T | D195Y (GAT→TAT) | kbaZ → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| RA | 3,297,739 | C→A | A134S (GCG→TCG) | yraQ ← | permease family protein YraQ |
| RA | 3,311,942 | C→A | G279V (GGA→GTA) | truB ← | tRNA pseudouridine(55) synthase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,395,380 | C→A | P293P (CCG→CCT) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,786,393 | G→T | E378D (GAG→GAT) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,994,856 | G→T | R32L (CGC→CTC) | dapF → | diaminopimelate epimerase |
| RA | 4,121,732 | G→T | P6T (CCA→ACA) | hslU ← | ATPase component of the HslVU protease |
| RA | 4,125,587 | G→T | I408I (ATC→ATA) | priA ← | primosome factor N' |
| RA | 4,228,109 | G→T | A127S (GCC→TCC) | yjbB → | putative inorganic phosphate export protein |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,269,433 | C→A | A7E (GCA→GAA) | aphA → | acid phosphatase/phosphotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,357,030 | G→T | P530T (CCG→ACG) | cadA ← | lysine decarboxylase 1 |
| RA | 4,413,619 | G→T | G198W (GGG→TGG) | yjfC → | putative acid‑‑amine ligase YjfC |
| RA | 4,491,339 | G→T | P396H (CCT→CAT) | idnT ← | L‑idonate/5‑ketogluconate/gluconate transporter |
| RA | 4,509,183 | C→A | pseudogene (175/471 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,574,648 | G→T | pseudogene (514/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102970 | 3104055 | 1086 | 27 [22] | [25] 27 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423767–3424234 | 3424525–3424238 | 5–759 | 26 [25] | [20] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 12 (0.130) | 134 (1.610) | 60/246 | 0.1 | 90.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.230) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.140) | 79 (0.950) | 50/246 | 0.3 | 83.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.230) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 110 (1.210) | 62/270 | 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 = | 151 (1.610) | 129 (1.380) | 60/276 | 0.2 | 62.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.060) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 116 (1.230) | 59/278 | 0.2 | 92.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.100) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||