mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 1,097,158 | C→T | 9.9% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| JC JC | 1,293,124 | IS5 (+) +4 bp | 9.1% | intergenic (‑202/‑400) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,355,064 | A→C | 43.8% | L136R (CTC→CGC) | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,356,852 | A→T | 5.7% | W87R (TGG→AGG) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| RA | 1,382,089 | A→G | 5.0% | D48G (GAT→GGT) | ompG → | outer membrane porin G |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,708,748 | G→C | 5.7% | A610A (GCG→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 8.3% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC JC | 1,907,448 | IS5 (–) +4 bp | 12.0% | coding (141‑144/144 nt) | yobF ← | DUF2527 family heat‑induced protein |
| RA | 1,907,573 | T→G | 44.2% | K7Q (AAA→CAA) | yobF ← | DUF2527 family heat‑induced protein |
| JC | 1,915,474 | Δ12 bp | 2.7% | coding (50‑61/699 nt) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,912,381 | G→A | 7.5% | P424L (CCG→CTG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 3,194,891 | T→A | 5.5% | intergenic (+66/‑250) | ibsD → / → ibsE | toxic membrane protein/toxic membrane protein |
| RA | 3,560,455 | +G | 94.6% | 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 | 3,950,469 | T→G | 8.1% | intergenic (+49/‑38) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 5.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 16.6% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 17.5% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 32.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.9% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 7.6% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 8.4% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,472,295 | T→G | 8.6% | N34T (AAC→ACC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583040 | 584610 | 1571 | 75 [71] | [71] 74 | [tfaX]–appY | [tfaX], appY |
| * | * | ÷ | NC_000913 | 2994988 | 2995543 | 556 | 72 [70] | [67] 73 | [ygeK]–[ygeN] | [ygeK], [ygeN] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 96 (0.660) | 65/526 | NT | 100% | intergenic (+8/‑769) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers | |||||
| * | ? | NC_000913 | 1096961 = | 94 (0.630) | 10 (0.090) | 3/382 | NT | 12.8% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 70 (0.660) | intergenic (+674/+62) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 73 (0.490) | 47 (0.330) | 32/510 | NT | 40.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 68 (0.480) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 69 (0.460) | 65 (0.460) | 46/510 | NT | 49.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 68 (0.480) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1242577 = | 128 (0.850) | 3 (0.020) | 3/506 | NT | 2.4% | coding (504/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | 1242595 = | 122 (0.870) | coding (486/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1299498 | 2 (0.010) | 60 (0.410) | 41/534 | NT | 98.4% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 54 (0.370) | 46/526 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 3381839 = | 172 (1.140) | 5 (0.030) | 5/524 | NT | 2.9% | coding (1097/1368 nt) | degQ | serine endoprotease, periplasmic |
| ? | NC_000913 | 3381869 = | 172 (1.180) | coding (1127/1368 nt) | degQ | serine endoprotease, periplasmic | |||||
| * | ? | NC_000913 | 3945979 = | 135 (0.900) | 3 (0.020) | 3/528 | NT | 2.2% | noncoding (2276/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | 4039784 = | NA (NA) | noncoding (2266/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 4034102 | 156 (1.040) | 3 (0.020) | 3/524 | NT | 1.9% | coding (958/1452 nt) | trkH | potassium transporter |
| ? | NC_000913 | = 4034172 | 163 (1.120) | coding (1028/1452 nt) | trkH | potassium transporter | |||||