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 |
| 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 | 2,312,212 | +TC | coding (538/1104 nt) | 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 | 4,114,469 | C→A | A2S (GCT→TCT) | fpr ← | ferredoxin‑NADP reductase; flavodoxin reductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1757086 | 1757430 | 345 | 76 [0] | [0] 38 | [pykF]–[lpp] | [pykF],[lpp] |
| * | * | ÷ | NC_000913 | 3423709–3424597 | 3424597 | 1–889 | 10 [6] | [8] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3875506 | 3875541 | 36 | 9 [8] | [8] 9 | yidX | putative lipoprotein |
| * | * | ÷ | NC_000913 | 4296108–4296379 | 4296385 | 7–278 | 9 [8] | [8] 9 | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 243009 | 36 (0.930) | 9 (0.260) | 6/116 | 2.3 | 20.2% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 39 (1.130) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 15 (0.480) | 7/104 | 1.8 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 555833 | 32 (0.830) | 6 (0.210) | 5/98 | 2.2 | 21.4% | coding (1223/1386 nt) | cysS | cysteinyl‑tRNA synthetase |
| ? | NC_000913 | = 556784 | 20 (0.680) | coding (90/213 nt) | ybcJ | ribosome‑associated protein; putative RNA‑binding protein | |||||
| * | ? | NC_000913 | 1207790 = | 4 (0.100) | 19 (0.650) | 12/98 | 0.7 | 88.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 2 (0.070) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 4 (0.100) | 18 (0.620) | 12/98 | 0.7 | 87.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 2 (0.070) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1287474 = | 24 (0.620) | 9 (0.260) | 7/114 | 2.0 | 29.9% | intergenic (‑146/+64) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287554 = | NA (NA) | noncoding (69/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1757085 | 0 (0.000) | 76 (1.960) | 28/130 | 0.1 | 100% | coding (1388/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1757431 = | 0 (0.000) | 37 (0.950) | 16/130 | 0.8 | 100% | coding (11/237 nt) | lpp | murein lipoprotein |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2277401 = | 34 (0.880) | 7 (0.210) | 5/110 | 2.5 | 20.4% | coding (1102/1590 nt) | yejF | microcin C ABC transporter ATPase |
| ? | NC_000913 | 2277552 = | 26 (0.790) | coding (1253/1590 nt) | yejF | microcin C ABC transporter ATPase | |||||
| * | ? | NC_000913 | 2803441 = | 57 (1.470) | 14 (0.430) | 4/110 | 2.9 | 23.9% | coding (2094/2145 nt) | nrdE | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| ? | NC_000913 | 2803529 = | 41 (1.250) | coding (28/960 nt) | nrdF | ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like protein | |||||
| * | ? | NC_000913 | = 3798325 | 33 (0.850) | 26 (0.700) | 6/124 | 2.5 | 35.0% | coding (988/1074 nt) | waaU | lipopolysaccharide core biosynthesis |
| ? | NC_000913 | = 3798516 | 65 (1.760) | coding (797/1074 nt) | waaU | lipopolysaccharide core biosynthesis | |||||
| * | ? | NC_000913 | 3927418 = | 19 (0.490) | 7 (0.220) | 5/106 | 2.4 | 30.1% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 17 (0.540) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | = 3927429 | 19 (0.490) | 5 (0.160) | 4/106 | 2.8 | 23.5% | coding (275/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | = 3927444 | 17 (0.540) | coding (290/993 nt) | asnA | asparagine synthetase A | |||||