mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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 | 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 | 1,756,796 | G→T | E367* (GAA→TAA) | pykF → | pyruvate kinase I |
| RA | 1,757,387 | C→G | intergenic (+277/‑34) | pykF → / → lpp | pyruvate kinase I/murein lipoprotein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 | 2,312,590 | G→A | Q54* (CAG→TAG) | ompC ← | outer membrane porin protein C |
| RA | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 3,413,571 | T→C | intergenic (‑106/‑293) | acrS ← / → acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| 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 | 4,114,419 | G→A | A18A (GCC→GCT) | fpr ← | ferredoxin‑NADP reductase; flavodoxin reductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423709–3424234 | 3424591–3424238 | 5–883 | 6 [3] | [3] 4 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 15989 = | NA (NA) | 5 (0.220) | 4/116 | 1.9 | NA | noncoding (603/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 16348 = | NA (NA) | noncoding (962/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 6 (0.290) | 6/106 | 1.2 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315644 = | NA (NA) | 19 (0.840) | 6/116 | 1.3 | NA | noncoding (416/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315712 = | NA (NA) | noncoding (484/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 382141 | NA (NA) | 5 (0.200) | 3/128 | 2.4 | NA | noncoding (882/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382258 | NA (NA) | noncoding (999/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 438152 | 18 (0.700) | 4 (0.190) | 4/106 | 1.7 | 22.0% | intergenic (‑17/+163) | yajO/dxs | 2‑carboxybenzaldehyde reductase/1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring |
| ? | NC_000913 | = 438293 | 14 (0.680) | intergenic (‑158/+22) | yajO/dxs | 2‑carboxybenzaldehyde reductase/1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring | |||||
| * | ? | NC_000913 | 1015208 = | 22 (0.850) | 7 (0.330) | 3/110 | 2.1 | 24.4% | coding (313/564 nt) | pqiC | DUF330 family putative lipoprotein |
| ? | NC_000913 | 1015844 = | 25 (1.160) | coding (130/168 nt) | rmf | ribosome modulation factor | |||||
| * | ? | NC_000913 | 1207790 = | 2 (0.080) | 17 (0.870) | 11/100 | 0.4 | 90.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 2 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 2 (0.080) | 12 (0.620) | 8/100 | 0.7 | 87.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 2 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1307027 = | 7 (0.270) | 3 (0.130) | 3/114 | 2.2 | 22.2% | coding (124/330 nt) | yciU | UPF0263 family protein |
| ? | NC_000913 | 1307124 = | 15 (0.670) | coding (27/330 nt) | yciU | UPF0263 family protein | |||||
| * | ? | NC_000913 | 1341858 = | 14 (0.540) | 5 (0.210) | 4/124 | 2.0 | 24.9% | intergenic (+131/‑63) | yciM/pyrF | LPS regulatory protein; putative modulator of LpxC proteolysis/orotidine‑5'‑phosphate decarboxylase |
| ? | NC_000913 | 1341945 = | 17 (0.700) | coding (25/738 nt) | pyrF | orotidine‑5'‑phosphate decarboxylase | |||||
| * | ? | NC_000913 | = 1387098 | 20 (0.770) | 7 (0.300) | 3/120 | 2.3 | 33.2% | coding (379/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| ? | NC_000913 | = 1387248 | 10 (0.430) | coding (529/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase | |||||
| * | ? | NC_000913 | 1466676 = | 14 (0.540) | 6 (0.260) | 3/116 | 2.2 | 22.1% | pseudogene (1285/2513 nt) | ydbA | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| ? | NC_000913 | 1466937 = | 30 (1.320) | pseudogene (1546/2513 nt) | ydbA | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913 | 1633763 = | NA (NA) | 4 (0.170) | 3/118 | 2.2 | 100% | coding (142/591 nt) | pinQ | Qin prophage; putative site‑specific recombinase |
| ? | NC_000913 | 1633785 = | 0 (0.000) | coding (164/591 nt) | pinQ | Qin prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | 1881698 = | 11 (0.430) | 3 (0.130) | 3/122 | 2.3 | 20.6% | coding (112/924 nt) | dmlR | transcriptional activator of dmlA |
| ? | NC_000913 | 1881770 = | 13 (0.540) | coding (40/924 nt) | dmlR | transcriptional activator of dmlA | |||||
| * | ? | NC_000913 | 2045242 = | 16 (0.620) | 8 (0.380) | 4/108 | 1.7 | 34.8% | coding (305/7077 nt) | yeeJ | putative adhesin |
| ? | NC_000913 | 2045355 = | 17 (0.810) | coding (418/7077 nt) | yeeJ | putative adhesin | |||||
| * | ? | NC_000913 | = 2236569 | 13 (0.500) | 3 (0.150) | 3/102 | 1.9 | 21.4% | noncoding (36/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | = 2236597 | 12 (0.600) | noncoding (64/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | 2632036 = | 21 (0.810) | 7 (0.300) | 4/118 | 1.9 | 33.5% | coding (500/1578 nt) | guaA | GMP synthetase (glutamine aminotransferase) |
| ? | NC_000913 | 2632263 = | 9 (0.390) | coding (273/1578 nt) | guaA | GMP synthetase (glutamine aminotransferase) | |||||
| * | ? | NC_000913 | = 2726279 | NA (NA) | 3 (0.130) | 3/122 | 2.3 | NA | intergenic (‑91/+2) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2726350 | NA (NA) | noncoding (2835/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | 3419891 = | 39 (1.510) | 6 (0.300) | 3/104 | 2.0 | 20.5% | pseudogene (785/960 nt) | yhdW | pseudogene, ABC transporter periplasmic binding protein family;putative transport; Not classified; putative periplasmic binding transport protein; periplasmic‑binding component of ABC superfamily |
| ? | NC_000913 | 3420220 = | 16 (0.790) | coding (87/1182 nt) | yhdX | putative amino acid ABC transporter permease | |||||
| * | ? | NC_000913 | 3620066 = | NA (NA) | 3 (0.150) | 3/104 | 2.0 | 100% | coding (875/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3620490 = | 0 (0.000) | coding (1299/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3798325 | 28 (1.080) | 14 (0.570) | 4/126 | 2.0 | 32.7% | coding (988/1074 nt) | waaU | lipopolysaccharide core biosynthesis |
| ? | NC_000913 | = 3798516 | 31 (1.260) | coding (797/1074 nt) | waaU | lipopolysaccharide core biosynthesis | |||||
| * | ? | NC_000913 | = 3831044 | 18 (0.700) | 8 (0.370) | 4/110 | 1.8 | 33.4% | coding (588/1710 nt) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| ? | NC_000913 | = 3831092 | 17 (0.790) | coding (636/1710 nt) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein | |||||
| * | ? | NC_000913 | = 3854888 | 14 (0.540) | 3 (0.130) | 3/114 | 2.2 | 21.4% | coding (967/1185 nt) | emrD | multidrug efflux system protein |
| ? | NC_000913 | = 3854930 | 10 (0.450) | coding (1009/1185 nt) | emrD | multidrug efflux system protein | |||||
| * | ? | NC_000913 | 3942313 = | NA (NA) | 3 (0.120) | 3/126 | 2.4 | NA | noncoding (506/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| ? | NC_000913 | 3942877 = | NA (NA) | noncoding (1070/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | 4153821 = | 27 (1.040) | 5 (0.220) | 4/114 | 1.8 | 20.3% | coding (1027/1152 nt) | argE | acetylornithine deacetylase |
| ? | NC_000913 | 4154127 = | 16 (0.720) | coding (721/1152 nt) | argE | acetylornithine deacetylase | |||||
| * | ? | NC_000913 | = 4542690 | 15 (0.580) | 7 (0.310) | 6/114 | 1.3 | 32.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 16 (0.720) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||