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 | 2,679,525 | 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 |
| RA | 3,585,681 | G→T | G381G (GGC→GGA) | ggt ← | gamma‑glutamyltranspeptidase |
| RA | 4,178,227 | T→G | V162G (GTT→GGT) | nusG → | transcription termination factor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 84032 | 84089 | 58 | 5 [4] | [4] 5 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | NC_000913 | 1168930 | 1168994 | 65 | 6 [4] | [2] 5 | ycfQ/bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
| * | * | ÷ | NC_000913 | 1958287 | 1958332 | 46 | 5 [4] | [4] 5 | torY/cutC | TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein |
| * | * | ÷ | NC_000913 | 2903755 | 2903863 | 109 | 5 [4] | [4] 5 | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| * | * | ÷ | NC_000913 | 3185266 | 3185344 | 79 | 5 [3] | [3] 5 | yqiC/ygiL | BMFP family putative fusogenic protein/putative fimbrial‑like adhesin protein |
| * | * | ÷ | NC_000913 | 3423719–3424234 | 3424594–3424238 | 5–876 | 6 [4] | [3] 6 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3799463 | 3799501 | 39 | 7 [4] | [4] 5 | waaZ | lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | NC_000913 | 4296108–4296380 | 4296392 | 13–285 | 6 [4] | [4] 7 | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | * | ÷ | NC_000913 | 4476968 | 4477060 | 93 | 5 [4] | [4] 5 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 105 (3.280) | 38/132 | 0.0 | 80.8% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 807574 | 25 (0.780) | coding (336/477 nt) | ybhB | kinase inhibitor homolog, UPF0098 family | |||||
| * | ? | NC_000913 | 771005 = | 10 (0.310) | 77 (2.410) | 35/132 | 0.0 | 88.5% | 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 | = 837655 | NA (NA) | 3 (0.100) | 3/122 | 2.7 | NA | noncoding (117/123 nt) | REP77 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP77 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | = 4326352 | NA (NA) | noncoding (551/583 nt) | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | = 1097101 | NA (NA) | 4 (0.140) | 4/116 | 2.2 | NA | intergenic (+272/+464) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097105 | NA (NA) | intergenic (+276/+460) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.780) | 12 (0.500) | 9/100 | 0.8 | 42.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.580) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.780) | 8 (0.330) | 8/100 | 1.0 | 32.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.580) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1508863 | NA (NA) | 4 (0.150) | 3/110 | 2.5 | 21.1% | coding (202/231 nt) | yncJ | uncharacterized protein |
| ? | NC_000913 | = 1508882 | 15 (0.560) | coding (183/231 nt) | yncJ | uncharacterized protein | |||||