mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 79,199 | C→G | S85S (TCG→TCC) | leuD ← | 3‑isopropylmalate dehydratase subunit LeuD |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 476,560 | C→A | noncoding (113/114 nt) | ffs → | signal recognition particle 4.5S RNA |
| RA | 549,903 | C→A | R93S (CGT→AGT) | ylbF → | DUF2877 domain‑containing protein YlbF |
| RA | 563,542 | C→A | V71V (GTC→GTA) | sfmF → | putative fimbrial protein SfmF |
| RA | 631,951 | G→T | M686I (ATG→ATT) | cstA → | carbon starvation protein A |
| RA | 693,687 | G→T | V423V (GTC→GTA) | miaB ← | isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 695,299 | G→T | G67W (GGG→TGG) | ubiF → | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol hydroxylase |
| RA | 768,319 | G→A | A114A (GCG→GCA) | mngB → | alpha‑mannosidase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,057,078 | C→A | A273D (GCT→GAT) | torT → | periplasmic trimethylamine‑N‑oxide binding protein |
| RA | 1,127,995 | C→A | R53S (CGT→AGT) | murJ → | putative lipid II flippase MurJ |
| 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 |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,216,193 | G→T | S42S (TCG→TCT) | ymgA → | putative two‑component system connector protein YmgA |
| RA | 1,264,275 | G→T | V188L (GTA→TTA) | hemA → | glutamyl‑tRNA reductase |
| RA | 1,361,985 | Δ1 bp | coding (75/558 nt) | puuR → | DNA‑binding transcriptional repressor PuuR |
| RA | 1,438,879 | G→C | P636A (CCT→GCT) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,527,144 | G→T | V69L (GTA→TTA) | yncH → | DUF5445 domain‑containing protein YncH |
| RA | 1,550,097 | G→T | E899D (GAG→GAT) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,650,156 | G→C | pseudogene (79/921 nt) | ydfE → | Qin prophage; protein YdfE |
| RA | 1,659,778 | C→A | D570E (GAC→GAA) | ynfE → | putative selenate reductase YnfE |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,787,454 | G→T | A4S (GCT→TCT) | ppsR → | posphoenolpyruvate synthetase regulatory protein |
| 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 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,265,187 | C→A | D37Y (GAT→TAT) | yeiW ← | PF03692 putative metal‑chelating domain‑containing protein YeiW |
| RA | 2,476,361 | G→T | A18S (GCT→TCT) | torI → | CPS‑53 (KpLE1) prophage; prophage CPS‑53 recombination directionality factor and response regulator inhibitor |
| RA | 2,498,595 | (T)5→4 | intergenic (‑300/‑76) | alaC ← / → ypdA | glutamate‑‑pyruvate aminotransferase AlaC/sensory histidine kinase YpdA |
| RA | 2,519,432 | G→T | A414E (GCG→GAG) | gltX ← | glutamate‑‑tRNA ligase |
| RA | 2,527,773 | C→A | G276G (GGC→GGA) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,529,424 | C→A | L251F (TTG→TTT) | ligA ← | DNA ligase |
| RA | 2,789,411 | G→A | V143I (GTC→ATC) | csiD → | PF08943 family protein CsiD |
| RA | 2,817,710 | G→T | intergenic (‑207/+74) | yqaB ← / ← argQ | fructose‑1‑phosphatase/tRNA‑Arg |
| RA | 2,945,316 | G→T | P176Q (CCG→CAG) | tcdA ← | tRNA threonylcarbamoyladenosine dehydratase |
| RA | 3,026,743 | G→T | T326T (ACG→ACT) | guaD → | guanine deaminase |
| RA | 3,036,906 | G→T | R401S (CGC→AGC) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,050,586 | G→T | L28M (CTG→ATG) | gcvT ← | aminomethyltransferase |
| RA | 3,062,862 | G→T | A671A (GCG→GCT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,140,113 | G→T | A69D (GCC→GAC) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,173,307 | G→A | A56T (GCA→ACA) | ygiN → | putative quinol monooxygenase YgiN |
| RA | 3,296,076 | G→T | A90S (GCC→TCC) | diaA → | DnaA initiator‑associating factor for replication initiation |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,355,928 | C→A | R402S (CGC→AGC) | gltB → | glutamate synthase subunit GltB |
| RA | 3,551,460 | G→T | S338R (AGC→AGA) | malP ← | maltodextrin phosphorylase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,606,940 | C→A | L164M (CTG→ATG) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,641,690 | G→T | E277* (GAA→TAA) | dtpB → | dipeptide/tripeptide:H(+) symporter DtpB |
| RA | 3,716,811 | C→A | R89S (CGC→AGC) | yiaD → | PF13488 family lipoprotein YiaD |
| RA | 3,722,186 | T→A | intergenic (+137/+142) | insK → / ← glyS | IS150 conserved protein InsB/glycine‑‑tRNA ligase subunit beta |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,975,694 | C→T | Y183Y (TAC→TAT) | wecE → | dTDP‑4‑dehydro‑6‑deoxy‑D‑glucose transaminase |
| RA | 4,110,467 | C→A | R180S (CGT→AGT) | cdh → | CDP‑diacylglycerol diphosphatase |
| RA | 4,146,311 | C→A | R18R (CGC→CGA) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,182,270 | T→G | D342E (GAT→GAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,228,142 | G→T | G138W (GGG→TGG) | yjbB → | putative inorganic phosphate export protein |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,279,334 | C→A | L286M (CTG→ATG) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,323,993 | C→A | W120C (TGG→TGT) | phnD ← | phosphonate ABC transporter periplasmic binding protein |
| RA | 4,328,168 | G→T | R345L (CGC→CTC) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,429,196 | C→T | L88L (CTG→TTG) | fklB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase FklB |
| RA | 4,496,413 | G→T | noncoding (9/85 nt) | leuX → | tRNA‑Leu |
| RA | 4,553,514 | C→A | A205E (GCG→GAG) | uxuB → | D‑mannonate oxidoreductase |
| RA | 4,589,875 | G→T | L469M (CTG→ATG) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,618,924 | C→T | G232G (GGC→GGT) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196265 | 1211431 | 15167 | 22 [21] | [18] 22 | [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 | 3102976 | 3104062 | 1087 | 22 [21] | [21] 22 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424533–3424239 | 7–764 | 25 [21] | [19] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 106 (1.440) | 64/270 | 0.0 | 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 = | 100 (1.320) | 116 (1.540) | 68/276 | 0.0 | 69.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 84 (1.110) | 57/278 | 0.1 | 95.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||