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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 482,230 | G→A | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,544,022 | 1 bp→AA | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 4,110,747 | G→T | intergenic (+62/+784) | cdh → / ← yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein |
| RA | 4,296,297 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,632 | C→A | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_pae_tpiA | 366327 | 366352 | 26 | 4 [0] | [1] 2 | lacZ/lacI | beta‑D‑galactosidase/lactose‑inducible lac operon transcriptional repressor |
| * | * | ÷ | NC_000913_3_pae_tpiA | 399220 | 399225 | 6 | 2 [1] | [0] 2 | yaiY | DUF2755 family inner membrane protein |
| * | * | ÷ | NC_000913_3_pae_tpiA | 525978–526703 | 526707 | 5–730 | 3 [1] | [1] 3 | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913_3_pae_tpiA | 572635 | 572690 | 56 | 3 [1] | [1] 2 | ybcN | DLP12 prophage; uncharacterized protein |
| * | * | ÷ | NC_000913_3_pae_tpiA | 678721 | 678756 | 36 | 2 [0] | [1] 3 | djlB | putative HscC co‑chaperone, uncharacterized J domain‑containing protein |
| * | * | ÷ | NC_000913_3_pae_tpiA | 698183 | 698210 | 28 | 3 [0] | [0] 3 | asnB | asparagine synthetase B |
| * | * | ÷ | NC_000913_3_pae_tpiA | 874371 | 874379 | 9 | 2 [1] | [0] 2 | yliE | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1159047 | 1159058 | 12 | 3 [1] | [0] 2 | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1312663 | 1312722 | 60 | 2 [1] | [1] 2 | yciB | IspA family inner membrane protein |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1367099 | 1367147 | 49 | 2 [0] | [1] 4 | pspF | psp operon transcriptional activator |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1905818 | 1905852 | 35 | 2 [0] | [1] 2 | mntP | putative Mn(2+) efflux pump, mntR‑regulated |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1982221 | 1982292 | 72 | 2 [1] | [1] 3 | otsB | trehalose‑6‑phosphate phosphatase, biosynthetic |
| * | * | ÷ | NC_000913_3_pae_tpiA | 2010691 | 2010702 | 12 | 3 [1] | [0] 2 | yedL | GNAT family putative N‑acetyltransferase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 2268782 | 2268840 | 59 | 2 [1] | [1] 3 | [yeiR] | [yeiR] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3138169 | 3138217 | 49 | 2 [1] | [1] 3 | gss | glutathionylspermidine amidase and glutathionylspermidine synthetase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3246883 | 3246900 | 18 | 3 [1] | [1] 2 | exuR | hexuronate regulon transcriptional repressor; autorepressor |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3423773–3424233 | 3424530–3424238 | 6–758 | 2 [1] | [1] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3440078 | 3440160 | 83 | 3 [1] | [1] 3 | rpoA | RNA polymerase, alpha subunit |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3647077 | 3647087 | 11 | 2 [1] | [0] 2 | gor | glutathione oxidoreductase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3651630 | 3651674 | 45 | 4 [0] | [0] 2 | yhiS | pseudogene |
| * | * | ÷ | NC_000913_3_pae_tpiA | 4630476 | 4630493 | 18 | 2 [1] | [1] 3 | ettA/slt | energy‑dependent translational throttle A/lytic murein transglycosylase, soluble |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 291400 | NA (NA) | 18 (1.170) | 16/246 | 0.2 | 90.1% | intergenic (‑54/‑4) | insA/yagJ | IS1 repressor TnpA/CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related |
| ? | NC_000913_3_pae_tpiA | 2490618 = | 2 (0.130) | coding (1333/1695 nt) | oxc | oxalyl CoA decarboxylase, ThDP‑dependent | |||||
| * | ? | NC_000913_3_pae_tpiA | 624579 = | 9 (0.580) | 4 (0.270) | 4/238 | 1.5 | 30.0% | intergenic (‑69/‑306) | fepB/entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| ? | NC_000913_3_pae_tpiA | 624602 = | 10 (0.670) | intergenic (‑92/‑283) | fepB/entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 | |||||
| * | ? | NC_000913_3_pae_tpiA | 1269102 = | NA (NA) | 5 (0.350) | 5/230 | 1.2 | 29.3% | intergenic (+83/+66) | kdsA/ldrA | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase/toxic polypeptide, small |
| ? | NC_000913_3_pae_tpiA | 1269110 = | 13 (0.840) | intergenic (+91/+58) | kdsA/ldrA | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase/toxic polypeptide, small | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1445179 | 15 (0.960) | 4 (0.280) | 4/230 | 1.4 | 22.3% | coding (2129/2640 nt) | ydbH | putative membrane‑anchored protein, function unknown |
| ? | NC_000913_3_pae_tpiA | = 1445190 | 14 (0.970) | coding (2140/2640 nt) | ydbH | putative membrane‑anchored protein, function unknown | |||||
| * | ? | NC_000913_3_pae_tpiA | 1622824 = | 14 (0.900) | 5 (0.340) | 5/236 | 1.2 | 29.1% | noncoding (91/98 nt) | mgrR | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent; affects sensitivity to antimicrobial peptides |
| ? | NC_000913_3_pae_tpiA | 1622844 = | 11 (0.740) | noncoding (71/98 nt) | mgrR | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent; affects sensitivity to antimicrobial peptides | |||||
| * | ? | NC_000913_3_pae_tpiA | 1975162 = | 12 (0.770) | 4 (0.270) | 4/236 | 1.5 | 26.3% | coding (163/1965 nt) | cheA | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
| ? | NC_000913_3_pae_tpiA | 1975189 = | 11 (0.740) | coding (136/1965 nt) | cheA | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein | |||||
| * | ? | NC_000913_3_pae_tpiA | 1978503 = | NA (NA) | 24 (1.540) | 22/248 | 0.1 | 96.0% | intergenic (‑306/+15) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913_3_pae_tpiA | = 2490627 | 1 (0.060) | coding (1324/1695 nt) | oxc | oxalyl CoA decarboxylase, ThDP‑dependent | |||||
| * | ? | NC_000913_3_pae_tpiA | = 2304676 | 7 (0.450) | 4 (0.270) | 4/234 | 1.4 | 40.8% | noncoding (260/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913_3_pae_tpiA | = 2304872 | 5 (0.340) | noncoding (456/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913_3_pae_tpiA | 2456281 = | 20 (1.290) | 4 (0.290) | 4/218 | 1.3 | 21.9% | intergenic (‑635/+46) | yfcV/sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| ? | NC_000913_3_pae_tpiA | 2456318 = | 11 (0.800) | intergenic (‑672/+9) | yfcV/sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 2684222 | NA (NA) | 4 (0.340) +30 bp |
4/188 | 1.1 | NA | intergenic (+166/+32) | yphH/glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| ? | NC_000913_3_pae_tpiA | = 3676286 | NA (NA) | intergenic (+178/+4) | yhjE/yhjG | putative MFS transporter; membrane protein/putative inner membrane‑anchored periplasmic AsmA family protein | |||||
| * | ? | NC_000913_3_pae_tpiA | 2725829 = | 19 (1.220) | 5 (0.340) | 5/232 | 1.2 | 24.5% | intergenic (‑83/+240) | kgtP/rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_tpiA | 2725849 = | 13 (0.890) | intergenic (‑103/+220) | kgtP/rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 3512511 = | NA (NA) | 3 (0.200) | 3/234 | 1.7 | NA | noncoding (1/90 nt) | REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_pae_tpiA | 3512536 = | NA (NA) | noncoding (26/90 nt) | REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP250 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3528142 | 8 (0.510) | 4 (0.280) | 4/228 | 1.4 | 31.6% | coding (1674/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein |
| ? | NC_000913_3_pae_tpiA | = 3528152 | 10 (0.700) | coding (1684/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913_3_pae_tpiA | 3570872 = | 17 (1.090) | 4 (0.270) | 3/236 | 1.7 | 20.9% | coding (448/1974 nt) | glgX | glycogen debranching enzyme |
| ? | NC_000913_3_pae_tpiA | 3570898 = | 14 (0.950) | coding (422/1974 nt) | glgX | glycogen debranching enzyme | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3916335 | 16 (1.030) | 4 (0.270) | 4/232 | 1.4 | 21.1% | coding (1041/1383 nt) | atpD | F1 sector of membrane‑bound ATP synthase, beta subunit |
| ? | NC_000913_3_pae_tpiA | = 3916349 | 15 (1.030) | coding (1027/1383 nt) | atpD | F1 sector of membrane‑bound ATP synthase, beta subunit | |||||
| * | ? | NC_000913_3_pae_tpiA | 4040817 = | NA (NA) | 6 (0.420) | 4/228 | 1.4 | NA | intergenic (+181/+89) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913_3_pae_tpiA | 4040841 = | NA (NA) | intergenic (+205/+65) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4454506 | 12 (0.770) | 3 (0.210) | 3/230 | 1.7 | 20.6% | intergenic (+12/+21) | yjfF/fbp | putative sugar ABC transporter permease/fructose‑1,6‑bisphosphatase I |
| ? | NC_000913_3_pae_tpiA | = 4454510 | 12 (0.830) | intergenic (+16/+17) | yjfF/fbp | putative sugar ABC transporter permease/fructose‑1,6‑bisphosphatase I | |||||