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 | 72,232 | A→G | G232G (GGT→GGC) | thiQ ← | thiamine ABC transporter ATP binding subunit |
| RA | 83,387 | G→A | P48L (CCC→CTC) | leuA ← | 2‑isopropylmalate synthase |
| RA | 99,288 | A→G | T296A (ACT→GCT) | ftsW → | putative lipid II flippase FtsW |
| RA | 117,201 | C→T | V117I (GTC→ATC) | ppdD ← | prepilin peptidase‑dependent protein |
| RA | 127,779 | A→G | intergenic (+192/‑133) | aceF → / → lpd | pyruvate dehydrogenase, E2 subunit/lipoamide dehydrogenase |
| RA | 150,732 | C→T | W74* (TGG→TGA) | yadC ← | fimbrial tip‑adhesin YadC |
| RA | 158,506 | T→C | V207V (GTA→GTG) | pcnB ← | poly(A) polymerase I |
| RA | 196,489 | A→G | V271V (GTA→GTG) | cdsA → | CDP‑diglyceride synthetase |
| RA | 203,524 | A→G | E59E (GAA→GAG) | lpxB → | lipid A disaccharide synthase |
| RA | 222,945 | C→T | A38V (GCC→GTC) | gmhB → | D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase |
| RA | 223,326 | C→T | A165V (GCA→GTA) | gmhB → | D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase |
| RA | 239,326 | C→T | pseudogene (137/189 nt) | yafF → | putative uncharacterized protein YafF |
| RA | 251,491 | Δ1 bp | coding (594/1056 nt) | dinB → | DNA polymerase IV |
| RA | 259,241 | A→G | V287A (GTC→GCC) | phoE ← | outer membrane porin PhoE |
| RA | 264,459 | C→T | V92I (GTC→ATC) | ykfG ← | CP4‑6 prophage; RadC‑like JAB domain‑containing protein YkfG |
| RA | 273,819 | (C)5→6 | coding (973/1146 nt) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 286,834 | T→C | S16P (TCC→CCC) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 291,412 | C→T | intergenic (‑66/‑88) | insA‑3 ← / → yagJ | IS1 protein InsA/CP4‑6 prophage; protein YagJ |
| RA | 321,564 | (G)7→8 | intergenic (+483/‑44) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 355,271 | C→T | A117V (GCC→GTC) | codB → | cytosine transporter |
| RA | 360,333 | A→G | K114K (AAA→AAG) | cynX → | cyanate transporter |
| RA | 363,490 | C→T | R939H (CGC→CAC) | lacZ ← | beta‑galactosidase |
| RA | 367,143 | A→T | I123N (ATC→AAC) | lacI ← | DNA‑binding transcriptional repressor LacI |
| RA | 375,638 | A→G | I60M (ATA→ATG) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,139 | A→G | V235A (GTG→GCG) | yaiO ← | outer membrane protein YaiO |
| RA | 407,827 | (G)5→6 | coding (400/678 nt) | aroM → | protein AroM |
| RA | 434,673 | T→C | A9A (GCT→GCC) | ribE → | 6,7‑dimethyl‑8‑ribityllumazine synthase |
| RA | 446,822 | A→G | V295A (GTG→GCG) | cyoE ← | heme O synthase |
| RA | 486,646 | G→A | S37S (TCG→TCA) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 529,055 | (T)8→7 | pseudogene (416/491 nt) | ybbD → | putative uncharacterized protein YbbD |
| RA | 543,198 | (A)7→8 | intergenic (+165/+63) | glxK → / ← allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase |
| RA | 561,800 | A→G | T702A (ACC→GCC) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 573,471 | A→G | Y34C (TAC→TGC) | rusA → | DLP12 prophage; crossover junction endodeoxyribonuclease RusA |
| RA | 627,215 | C→T | R382R (CGC→CGT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| RA | 630,002 | A→G | I37V (ATT→GTT) | cstA → | carbon starvation protein A |
| RA | 685,941 | (C)6→7 | coding (729/741 nt) | gltJ ← | glutamate/aspartate ABC transporter membrane subunit GltJ |
| RA | 724,997 | A→G | G680G (GGT→GGC) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 824,318 | A→G | H60H (CAT→CAC) | ybhP ← | endonuclease/exonuclease/phosphatase domain‑containing protein YbhP |
| RA | 1,002,224 | (G)7→8 | coding (418/1071 nt) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,091,349 | (C)5→6 | coding (941/2424 nt) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin |
| RA | 1,138,175 | (G)5→6 | coding (805/942 nt) | flgJ → | putative peptidoglycan hydrolase FlgJ |
| RA | 1,209,497 | T→C | pseudogene (159/537 nt) | stfE ← | e14 prophage; putative side tail fiber protein fragment |
| RA | 1,224,612 | T→C | E250E (GAA→GAG) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,335,599 | T→C | S10P (TCC→CCC) | ymiC → | protein YmiC |
| RA | 1,339,446 | A→G | K39K (AAA→AAG) | pgpB → | phosphatidylglycerophosphatase B |
| RA | 1,360,639 | A→G | G90G (GGT→GGC) | puuA ← | glutamate‑putrescine ligase |
| RA | 1,403,104 | C→T | G51D (GGC→GAC) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase subunit B |
| RA | 1,414,053 | C→T | L247L (CTG→CTA) | recT ← | Rac prophage; recombinase, DNA renaturation |
| RA | 1,418,185 | A→G | C15C (TGT→TGC) | kilR ← | Rac prophage; inhibitor of FtsZ, killing protein |
| RA | 1,479,687 | (G)6→7 | coding (550/1758 nt) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,569,394 | A→G | S366P (TCC→CCC) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,575,405 | A→G | S739P (TCC→CCC) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,604,150 | T→C | L35S (TTG→TCG) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,655,360 | (C)5→6 | coding (314/327 nt) | ynfA ← | conserved inner membrane protein YnfA |
| RA | 1,712,518 | (C)6→7 | intergenic (+360/‑251) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,738,767 | T→C | R308R (CGT→CGC) | purR → | DNA‑binding transcriptional repressor PurR |
| RA | 1,765,413 | T→C | T74A (ACC→GCC) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 2,004,386 | G→A | G172D (GGT→GAT) | fliD → | flagellar filament capping protein |
| RA | 2,048,065 | T→C | V1043A (GTT→GCT) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,054,441 | T→C | Y267H (TAC→CAC) | shiA → | shikimate:H(+) symporter |
| RA | 2,222,595 | A→G | E137E (GAA→GAG) | dld → | D‑lactate dehydrogenase |
| RA | 2,237,776 | T→C | H505R (CAC→CGC) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,250,434 | T→C | F240L (TTC→CTC) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,274,125 | T→C | Y588H (TAT→CAT) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,284,237 | T→C | L37L (TTA→CTA) | yejL → | DUF1414 domain‑containing protein YejL |
| RA | 2,360,462 | (C)5→6 | coding (953/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,363,234 | T→C | T134A (ACC→GCC) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,385,021 | T→C | P234P (CCA→CCG) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,442,210 | G→A | T149T (ACG→ACA) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,527,731 | T→C | I262I (ATT→ATC) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,612,921 | A→G | N341S (AAT→AGT) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,652,086 | T→C | T68A (ACA→GCA) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,664,775 | T→C | L129P (CTG→CCG) | yfhR → | putative peptidase |
| RA | 2,677,867 | C→T | K165K (AAG→AAA) | yphE ← | putative ABC transporter ATP‑binding protein YphE |
| RA | 2,839,028 | T→C | L79L (TTA→TTG) | ascG ← | DNA‑binding transcriptional repressor AscG |
| RA | 2,862,680 | G→A | A116T (GCC→ACC) | ygbK → | putative 3‑oxo‑tetronate kinase YgbK |
| RA | 2,877,945 | (C)6→7 | intergenic (+327/+624) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,945,682 | A→T | I54N (ATT→AAT) | tcdA ← | tRNA threonylcarbamoyladenosine dehydratase |
| RA | 2,982,176 | T→C | T3A (ACT→GCT) | araE ← | arabinose:H(+) symporter |
| RA | 3,020,957 | T→C | Y140H (TAC→CAC) | ygfM → | putative oxidoreductase |
| RA | 3,180,431 | T→C | V4A (GTC→GCC) | ygiC → | putative enzyme with ATPase activity |
| RA | 3,199,036 | Δ1 bp | coding (606/2841 nt) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,213,306 | T→C | V87A (GTG→GCG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,260,941 | A→G | V493A (GTG→GCG) | tdcE ← | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| RA | 3,302,197 | T→C | V238A (GTG→GCG) | yhbU → | putative peptidase YhbU |
| RA | 3,345,926 | T→C | S404P (TCC→CCC) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| RA | 3,365,344 | A→G | pseudogene (160/371 nt) | yhcE → | putative uncharacterized protein YhcE |
| RA | 3,521,187 | A→G | V88A (GTT→GCT) | hofO ← | DNA utilization protein HofO |
| RA | 3,532,857 | G→A | A14T (GCT→ACT) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,564,531 | T→C | H684R (CAT→CGT) | glgP ← | glycogen phosphorylase |
| RA | 3,565,412 | G→A | D390D (GAC→GAT) | glgP ← | glycogen phosphorylase |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,631,169 | T→C | E474E (GAA→GAG) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,721,373 | G→A | G59E (GGA→GAA) | insK → | IS150 conserved protein InsB |
| RA | 3,757,963 | (T)7→8 | intergenic (‑136/+54) | yiaY ← / ← selB | L‑threonine dehydrogenase/selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,800,833 | T→C | T45A (ACA→GCA) | waaY ← | lipopolysaccharide core heptose (II) kinase |
| RA | 3,895,717 | T→C | D298G (GAC→GGC) | adeP ← | adenine:H(+) symporter |
| RA | 3,914,196 | A→G | G335G (GGT→GGC) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | 3,924,017 | C→T | A539A (GCG→GCA) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,926,975 | T→C | D10G (GAC→GGC) | asnC ← | DNA‑binding transcriptional dual regulator AsnC |
| RA | 3,928,950 | C→T | Q218Q (CAG→CAA) | viaA ← | protein ViaA |
| RA | 4,042,378 | T→C | intergenic (+40/‑37) | yihD → / → srkA | conserved protein YihD/stress response kinase A |
| RA | 4,073,577 | T→C | intergenic (‑6/‑162) | yihU ← / → yihV | 3‑sulfolactaldehyde reductase/6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,248,236 | T→C | V89A (GTG→GCG) | lamB → | maltose outer membrane channel/phage lambda receptor protein |
| RA | 4,289,148 | T→C | V462A (GTG→GCG) | nrfA → | 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 | 4,397,786 | C→T | A125A (GCC→GCT) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,602,033 | A→G | V22A (GTC→GCC) | yjjB ← | putative succinate exporter YjjB |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361198 | 361910 | 713 | 250 [241] | [241] 252 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856995 | 2857095 | 101 | 244 [240] | [0] 374 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423689–3424234 | 3424615–3424238 | 5–927 | 243 [238] | [240] 248 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 400 (1.050) | 354 (0.960) | 162/190 | 0.1 | 64.6% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | 1207790 = | 195 (0.510) | 212 (0.670) | 121/164 | 1.5 | 58.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 134 (0.420) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4556760 | 139 (0.400) | 287 (0.780) +TTT |
127/172 | 1.5 | 66.1% | coding (107/144 nt) | ytiD | protein YtiD |
| ? | NC_000913 | 4556761 = | 151 (0.400) | coding (108/144 nt) | ytiD | protein YtiD | |||||