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 |
| 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 |
| JC JC | 3,311,380 | IS4 (+) +12 bp | noncoding (156‑167/174 nt) | psrO → | novel sRNA, function unknown |
| 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 | 3424589–3424238 | 5–881 | 10 [2] | [1] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3781151 | 3781181 | 31 | 3 [1] | [2] 3 | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | * | ÷ | NC_000913 | 4136576 | 4136581 | 6 | 7 [2] | [0] 6 | yijE | EamA‑like transporter family protein |
| * | * | ÷ | NC_000913 | 4296120–4296378 | 4296397 | 20–278 | 4 [2] | [2] 5 | 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 | 225456 = | NA (NA) | 3 (0.170) | 3/114 | 1.7 | NA | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | 225477 = | NA (NA) | intergenic (+20/‑23) | ileV/alaV | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NC_000913 | = 243009 | 12 (0.600) | 4 (0.220) | 3/118 | 1.8 | 24.5% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 14 (0.790) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 7 (0.440) | 6/106 | 0.8 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 381375 | NA (NA) | 4 (0.220) | 3/118 | 1.8 | NA | noncoding (116/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381732 | NA (NA) | noncoding (473/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381480 | NA (NA) | 5 (0.260) | 3/126 | 1.9 | NA | noncoding (221/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381788 | NA (NA) | noncoding (529/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382153 | NA (NA) | 6 (0.330) | 3/120 | 1.8 | NA | noncoding (894/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382246 | NA (NA) | noncoding (987/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 715563 | 22 (1.100) | 5 (0.300) | 4/112 | 1.4 | 24.0% | coding (152/495 nt) | ybfP | lipoprotein |
| ? | NC_000913 | = 715719 | 13 (0.770) | coding (308/495 nt) | ybfP | lipoprotein | |||||
| * | ? | NC_000913 | 726474 = | 11 (0.550) | 3 (0.160) | 3/122 | 1.8 | 22.8% | coding (563/2049 nt) | kdpB | potassium translocating ATPase, subunit B |
| ? | NC_000913 | 3621273 = | NA (NA) | coding (2082/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 857638 = | NA (NA) | 13 (0.730) | 5/118 | 1.2 | 36.1% | noncoding (23/98 nt) | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 857687 = | 23 (1.290) | noncoding (72/98 nt) | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 992353 | 14 (0.700) | 3 (0.170) | 3/116 | 1.7 | 22.8% | coding (1732/2613 nt) | pepN | aminopeptidase N |
| ? | NC_000913 | = 992429 | 8 (0.460) | coding (1808/2613 nt) | pepN | aminopeptidase N | |||||
| * | ? | NC_000913 | = 1207805 | 22 (1.100) | 5 (0.330) | 5/100 | 1.0 | 26.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 11 (0.730) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 26 (1.390) | 19/124 | 0.1 | 100% | 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 | 1362001 = | 20 (1.000) | 6 (0.350) | 4/114 | 1.4 | 28.4% | coding (91/558 nt) | puuR | repressor for the divergent puu operons, putrescine inducible |
| ? | NC_000913 | 1362051 = | 13 (0.760) | coding (141/558 nt) | puuR | repressor for the divergent puu operons, putrescine inducible | |||||
| * | ? | NC_000913 | 1683535 = | 20 (1.000) | 4 (0.230) | 3/114 | 1.7 | 24.1% | coding (654/1302 nt) | rstB | sensory histidine kinase of RstAB two‑component system |
| ? | NC_000913 | 1683597 = | 8 (0.470) | coding (716/1302 nt) | rstB | sensory histidine kinase of RstAB two‑component system | |||||
| * | ? | NC_000913 | = 1792600 | 16 (0.800) | 6 (0.340) | 3/118 | 1.8 | 27.7% | coding (132/465 nt) | nlpC | putative C40 clan peptidase lipoprotein |
| ? | NC_000913 | = 1792651 | 17 (0.950) | coding (81/465 nt) | nlpC | putative C40 clan peptidase lipoprotein | |||||
| * | ? | NC_000913 | 2077808 = | 13 (0.650) | 5 (0.310) | 4/108 | 1.3 | 20.2% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 29 (1.780) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3071424 | 14 (0.700) | 5 (0.290) | 3/116 | 1.7 | 23.6% | intergenic (‑180/+35) | fbaA/pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| ? | NC_000913 | = 3071467 | 20 (1.140) | coding (1156/1164 nt) | pgk | phosphoglycerate kinase | |||||
| * | ? | NC_000913 | 3091309 = | 11 (0.550) | 4 (0.220) | 3/118 | 1.8 | 25.1% | coding (176/732 nt) | rsmE | 16S rRNA m(3)U1498 methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3091468 = | 14 (0.790) | coding (335/732 nt) | rsmE | 16S rRNA m(3)U1498 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 3408870 | 12 (0.600) | 4 (0.230) | 4/116 | 1.4 | 32.6% | coding (1264/1452 nt) | panF | pantothenate:sodium symporter |
| ? | NC_000913 | = 3408895 | 6 (0.340) | coding (1289/1452 nt) | panF | pantothenate:sodium symporter | |||||
| * | ? | NC_000913 | = 3614604 | 17 (0.850) | 5 (0.280) | 3/118 | 1.8 | 23.7% | coding (938/1575 nt) | nikA | nickel/heme ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 3615035 | 17 (0.950) | coding (1369/1575 nt) | nikA | nickel/heme ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 3621973 | NA (NA) | 4 (0.230) | 3/114 | 1.7 | NA | coding (2782/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3622055 | NA (NA) | coding (2864/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3625629 = | NA (NA) | 4 (0.220) | 4/120 | 1.5 | 40.0% | noncoding (41/82 nt) | RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP260 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3625675 = | 6 (0.330) | intergenic (+161/+4) | yhhI/yhhJ | putative transposase/putative ABC transporter permease | |||||
| * | ? | NC_000913 | = 3798325 | 21 (1.050) | 8 (0.420) | 4/126 | 1.6 | 26.7% | coding (988/1074 nt) | waaU | lipopolysaccharide core biosynthesis |
| ? | NC_000913 | = 3798516 | 24 (1.260) | coding (797/1074 nt) | waaU | lipopolysaccharide core biosynthesis | |||||
| * | ? | NC_000913 | 4341778 = | 16 (0.800) | 5 (0.350) | 3/96 | 1.4 | 39.1% | intergenic (‑150/‑133) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding |
| ? | NC_000913 | 4341834 = | 4 (0.280) | intergenic (‑206/‑77) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding | |||||