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 | 2,312,590 | 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 |
| 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 |
| RA | 4,114,456 | G→A | T6I (ACA→ATA) | fpr ← | ferredoxin‑NADP reductase; flavodoxin reductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583319 | 583338 | 20 | 4 [1] | [0] 2 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | NC_000913 | 583521 | 583541 | 21 | 2 [1] | [1] 2 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | NC_000913 | 777121 | 777128 | 8 | 2 [0] | [0] 2 | tolA | membrane anchored protein in TolA‑TolQ‑TolR complex |
| * | * | ÷ | NC_000913 | 1012464 | 1012478 | 15 | 2 [1] | [1] 2 | pqiA | paraquat‑inducible, SoxRS‑regulated inner membrane protein |
| * | * | ÷ | NC_000913 | 1024871 | 1024883 | 13 | 2 [1] | [1] 2 | helD | DNA helicase IV |
| * | * | ÷ | NC_000913 | 1128415 | 1128442 | 28 | 2 [1] | [1] 2 | murJ | putative lipid II flippase |
| * | * | ÷ | NC_000913 | 1191811 | 1191829 | 19 | 2 [1] | [1] 2 | purB | adenylosuccinate lyase |
| * | * | ÷ | NC_000913 | 1530073 | 1530096 | 24 | 2 [1] | [1] 2 | ydcD | putative immunity protein for RhsE |
| * | * | ÷ | NC_000913 | 2470238 | 2470266 | 29 | 2 [1] | [1] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2774393 | 2774402 | 10 | 2 [1] | [1] 2 | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | * | ÷ | NC_000913 | 3360924 | 3360944 | 21 | 2 [1] | [1] 4 | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein |
| * | * | ÷ | NC_000913 | 3423718–3424234 | 3424589–3424238 | 5–872 | 2 [0] | [1] 4 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3769789 | 3769827 | 39 | 2 [0] | [1] 2 | yibV/yibU | pseudogene, putative cryptic Rhs immunity protein/pseudogene, H repeat‑associated protein |
| * | * | ÷ | NC_000913 | 3847509 | 3847526 | 18 | 2 [1] | [0] 3 | uhpC | membrane protein regulates uhpT expression |
| * | * | ÷ | NC_000913 | 3887015 | 3887023 | 9 | 2 [1] | [1] 2 | mnmE | tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase |
| * | * | ÷ | NC_000913 | 3906796 | 3906808 | 13 | 3 [1] | [0] 3 | bglG/phoU | transcriptional antiterminator of the bgl operon/negative regulator of PhoR/PhoB two‑component regulator |
| * | * | ÷ | NC_000913 | 4008297 | 4008311 | 15 | 3 [1] | [1] 4 | rhtC | threonine efflux pump |
| * | * | ÷ | NC_000913 | 4296098–4296380 | 4296387 | 8–290 | 9 [1] | [1] 2 | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | * | ÷ | NC_000913 | 4326926 | 4326937 | 12 | 2 [1] | [1] 2 | yjdM/crfC | zinc‑ribbon family protein/clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 235667 | 8 (0.420) | 3 (0.190) | 3/112 | 1.5 | 35.8% | coding (336/468 nt) | rnhA | ribonuclease HI, degrades RNA of DNA‑RNA hybrids |
| ? | NC_000913 | = 235673 | 4 (0.250) | coding (330/468 nt) | rnhA | ribonuclease HI, degrades RNA of DNA‑RNA hybrids | |||||
| * | ? | NC_000913 | 969360 = | 10 (0.530) | 3 (0.180) | 3/114 | 1.5 | 27.8% | intergenic (+8/‑29) | lpxK/ycaQ | lipid A 4'kinase/DUF1006 family protein with C‑terminal wHTH domain |
| ? | NC_000913 | 969402 = | 7 (0.430) | coding (14/1233 nt) | ycaQ | DUF1006 family protein with C‑terminal wHTH domain | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.320) | 13 (0.910) | 11/100 | 0.2 | 77.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.210) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.320) | 8 (0.560) | 5/100 | 0.8 | 68.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.210) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3619916 = | NA (NA) | 3 (0.170) | 3/126 | 1.6 | NA | coding (725/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619969 = | NA (NA) | coding (778/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||