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] | |
| 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 | 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 | 1673455 | 1676610 | 3156 | 297 [295] | [296] 297 | [mdtJ]–[pntA] | [mdtJ], tqsA, pntB, [pntA] |
| * | * | ÷ | NC_000913 | 3423675–3424234 | 3424602–3424238 | 5–928 | 297 [295] | [294] 297 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 381 (0.870) | 169/300 | 2.0 | 62.7% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 565828 | 227 (0.520) | coding (151/1164 nt) | intD | DLP12 prophage; putative phage integrase | |||||
| * | ? | NC_000913 | 1094245 = | NA (NA) | 225 (0.510) | 161/300 | 2.7 | 44.9% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 1199869 = | 276 (0.630) | coding (938/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | 1207790 = | 71 (0.160) | 273 (0.700) | 163/268 | 1.0 | 79.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 78 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 72 (0.160) | 254 (0.650) | 158/268 | 1.4 | 78.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 78 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 483 (1.130) | 232/292 | 0.0 | 99.9% | 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 | 1399590 = | 222 (0.510) | 292 (0.670) | 163/300 | 2.5 | 56.8% | intergenic (‑64/+131) | fnr/ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1399593 | 230 (0.530) | 372 (0.860) | 158/298 | 2.9 | 61.8% | intergenic (‑67/+128) | fnr/ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 273 (0.620) | 168/300 | 2.1 | 51.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4434629 = | 260 (0.590) | coding (1937/1944 nt) | cpdB | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 240 (0.550) | 164/298 | 2.3 | 46.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 279 (0.640) | coding (13/597 nt) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA | |||||
| * | ? | NC_000913 | 4542682 = | 237 (0.540) | 279 (0.680) | 183/282 | 0.5 | 53.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 258 (0.630) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 237 (0.540) | 252 (0.610) | 164/282 | 1.5 | 51.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 258 (0.630) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||