mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
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] | |
| JC | 1,673,557 | Δ120 bp | intergenic (‑56/‑237) | mdtJ ← / → tqsA | multidrug efflux system transporter/pheromone AI‑2 transporter |
| 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 | 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 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1673532 | 1673677 | 146 | 264 [238] | [249] 254 | mdtJ/tqsA | multidrug efflux system transporter/pheromone AI‑2 transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 308 (0.600) | 160/300 | 2.3 | 51.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 295085 | 295 (0.570) | intergenic (‑286/+54) | yagM/yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 394 (0.770) | 177/300 | 1.4 | 60.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 565828 | 253 (0.490) | coding (151/1164 nt) | intD | DLP12 prophage; putative phage integrase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 281 (0.550) | 178/300 | 1.3 | 49.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 295082 = | 283 (0.550) | intergenic (‑283/+57) | yagM/yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 464 (0.900) | 166/300 | 1.9 | 63.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 577188 = | 263 (0.510) | intergenic (‑363/‑210) | nmpC/essD | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein | |||||
| * | ? | NC_000913 | 677185 = | 258 (0.500) | 233 (0.480) | 162/284 | 1.7 | 49.6% | coding (475/708 nt) | ybeR | uncharacterized protein |
| ? | NC_000913 | = 677214 | 229 (0.470) | coding (504/708 nt) | ybeR | uncharacterized protein | |||||
| * | ? | NC_000913 | 1094245 = | NA (NA) | 267 (0.520) | 164/300 | 2.0 | 53.6% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1199869 = | 231 (0.450) | coding (938/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | = 1095502 | NA (NA) | 266 (0.520) | 168/298 | 1.8 | 54.1% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 1199871 | 226 (0.440) | coding (936/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | 1207790 = | 43 (0.080) | 354 (0.770) | 185/268 | 0.4 | 88.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 54 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 44 (0.090) | 342 (0.740) | 184/268 | 0.4 | 88.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 54 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.000) | 521 (1.040) | 233/292 | 0.0 | 99.8% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 1 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1909928 | 251 (0.490) | 248 (0.490) | 149/296 | 2.8 | 49.7% | coding (172/792 nt) | kdgR | KDG regulon transcriptional repressor |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 1 (0.000) | 501 (1.030) | 227/284 | 0.0 | 99.9% | 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 | 1978503 = | NA (NA) | 300 (0.580) | 166/300 | 1.9 | NA | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4434636 | NA (NA) | coding (1930/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | 2101749 = | NA (NA) | 341 (0.660) | 170/300 | 1.7 | 55.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2174359 = | 270 (0.520) | coding (208/285 nt) | gatB | galactitol‑specific enzyme IIB component of PTS | |||||
| * | ? | NC_000913 | = 2558698 | 219 (0.430) | 242 (0.500) | 154/284 | 2.1 | 52.9% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase, large subunit, heavy chain/CPZ‑55 prophage; putative phage integrase |
| ? | NC_000913 | 2565489 = | 223 (0.460) | coding (1396/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | NC_000913 | 3393149 = | 312 (0.610) | 312 (0.610) | 182/300 | 1.2 | 50.0% | coding (3110/3801 nt) | yhdP | DUF3971‑AsmA2 domains protein |
| ? | NC_000913 | = 3584195 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 3393157 | 304 (0.590) | 347 (0.670) | 182/300 | 1.2 | 53.3% | coding (3102/3801 nt) | yhdP | DUF3971‑AsmA2 domains protein |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 253 (0.490) | 156/300 | 2.5 | 46.5% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4434629 = | 291 (0.570) | coding (1937/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 314 (0.610) | 184/298 | 1.0 | 51.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 292 (0.570) | coding (13/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 289 (0.560) | 169/300 | 1.8 | 49.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542042 = | 298 (0.580) | coding (6/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||
| * | ? | NC_000913 | = 4020781 | 273 (0.530) | 267 (0.520) | 177/300 | 1.4 | 49.7% | coding (556/1641 nt) | ubiB | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase |
| ? | NC_000913 | 4020794 = | 267 (0.520) | coding (569/1641 nt) | ubiB | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase | |||||
| * | ? | NC_000913 | 4542682 = | 281 (0.550) | 349 (0.720) | 192/282 | 0.5 | 56.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 267 (0.550) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 281 (0.550) | 314 (0.650) | 179/282 | 0.9 | 54.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 267 (0.550) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||