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 |
| JC JC | 486,122 | IS1 (–) +8 bp | coding (362‑369/648 nt) | acrR → | transcriptional repressor |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| 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 | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,811,095 | A→C | D109A (GAT→GCT) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1630446 | 1630497 | 52 | 3 [1] | [1] 2 | ydfI | putative NAD‑dependent D‑mannonate oxidoreductase |
| * | * | ÷ | NC_000913 | 2374795 | 2374874 | 80 | 2 [1] | [1] 3 | menE | O‑succinylbenzoate‑CoA ligase |
| * | * | ÷ | NC_000913 | 2572549 | 2572553 | 5 | 3 [1] | [0] 2 | eutD | phosphate acetyltransferase |
| * | * | ÷ | NC_000913 | 3162355 | 3162364 | 10 | 2 [1] | [0] 2 | ftsP | septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts) |
| * | * | ÷ | NC_000913 | 3423723–3424234 | 3424593–3424238 | 5–871 | 2 [1] | [1] 2 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3849615 | 3849638 | 24 | 2 [0] | [1] 3 | uhpB | sensory histidine kinase in two‑component regulatory sytem with UhpA |
| * | * | ÷ | NC_000913 | 4235750 | 4235760 | 11 | 2 [1] | [1] 2 | pgi/yjbE | glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein |
| * | * | ÷ | NC_000913 | 4296113–4296378 | 4296392 | 15–280 | 2 [1] | [1] 2 | 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 | 224412 = | NA (NA) | 3 (0.180) | 3/118 | 1.6 | NA | noncoding (642/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 224936 = | NA (NA) | noncoding (1166/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 33 (1.780) | 19/132 | 0.1 | 62.3% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 807574 | 20 (1.080) | coding (336/477 nt) | ybhB | kinase inhibitor homolog, UPF0098 family | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 4 (0.270) | 4/106 | 1.1 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 355486 | 17 (0.920) | 3 (0.180) | 3/118 | 1.6 | 21.3% | coding (565/1260 nt) | codB | cytosine transporter |
| ? | NC_000913 | = 355537 | 7 (0.420) | coding (616/1260 nt) | codB | cytosine transporter | |||||
| * | ? | NC_000913 | 771005 = | 9 (0.480) | 27 (1.450) | 19/132 | 0.1 | 75.0% | intergenic (+394/‑453) | mngB/cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| ? | NC_000913 | = 1050545 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 30 (1.720) | 22/124 | 0.0 | 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 | 1492172 = | 10 (0.540) | 3 (0.180) | 3/118 | 1.6 | 27.4% | noncoding (54/56 nt) | sokB | sRNA antisense regulator blocking mokB, and hence hokB, translation |
| ? | NC_000913 | 1492206 = | 7 (0.420) | intergenic (+32/‑264) | sokB/trg | sRNA antisense regulator blocking mokB, and hence hokB, translation/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor | |||||
| * | ? | NC_000913 | = 1636407 | 5 (0.270) | 4 (0.290) | 3/100 | 1.3 | 42.6% | intergenic (‑40/‑349) | nohQ/ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| ? | NC_000913 | = 1636432 | 7 (0.500) | intergenic (‑65/‑324) | nohQ/ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage | |||||
| * | ? | NC_000913 | = 3234660 | 10 (0.660) | 4 (0.260) | 3/108 | 1.4 | 28.6% | noncoding (23/86 nt) | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 3234703 | NA (NA) | noncoding (66/86 nt) | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 3355606 | 12 (0.650) | 5 (0.310) | 4/116 | 1.3 | 24.7% | coding (882/4461 nt) | gltB | glutamate synthase, large subunit |
| ? | NC_000913 | = 3355642 | 20 (1.230) | coding (918/4461 nt) | gltB | glutamate synthase, large subunit | |||||
| * | ? | NC_000913 | 3927418 = | 17 (0.920) | 6 (0.400) | 4/108 | 1.2 | 29.4% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 15 (0.990) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||