mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 40.9% | 33.2 / 48.0 | 44 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 126,970 | 0 | G | C | 27.3% | 33.5 / 14.8 | 22 | V426L (GTT→CTT) | aceF | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| * | NC_000913 | 3,360,644 | 0 | G | C | 26.1% | 34.5 / 14.9 | 23 | intergenic (+28/‑532) | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein |
| * | NC_000913 | 3,360,645 | 0 | T | A | 26.1% | 31.6 / 12.6 | 23 | intergenic (+29/‑531) | gltD/gltF | glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein |
| * | NC_000913 | 124,744 | 0 | T | . | 23.3% | 112.2 / 31.4 | 43 | coding (1728/2664 nt) | aceE | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| * | NC_000913 | 3,596,223 | 0 | G | C | 23.1% | 50.6 / 14.7 | 26 | L61V (CTG→GTG) | livH | branched‑chain amino acid ABC transporter permease |
| * | NC_000913 | 3,596,228 | 0 | G | C | 23.1% | 52.2 / 14.3 | 26 | A59G (GCC→GGC) ‡ | livH | branched‑chain amino acid ABC transporter permease |
| * | NC_000913 | 3,596,229 | 0 | C | T | 23.1% | 45.3 / 10.4 | 26 | A59T (GCC→ACC) ‡ | livH | branched‑chain amino acid ABC transporter permease |
| * | NC_000913 | 120,158 | 1 | . | A | 21.4% | 62.4 / 24.0 | 28 | intergenic (+23/+20) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| * | NC_000913 | 1,642,370 | 0 | C | G | 21.1% | 87.6 / 19.5 | 38 | intergenic (+303/+119) | cspF/quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| * | NC_000913 | 1,642,373 | 0 | C | G | 21.1% | 91.1 / 17.3 | 38 | intergenic (+306/+116) | cspF/quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| * | NC_000913 | 120,154 | 0 | T | . | 20.7% | 77.2 / 16.3 | 29 | intergenic (+19/+24) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| Marginal new junction evidence (lowest skew 10 of 37 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2078529 | 29 (0.870) | 7 (0.230) | 7/240 | 2.6 | 19.8% | intergenic (+422/+20) | yeeW/yoeD | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related |
| ? | NC_000913 | = 2078541 | 30 (0.980) | intergenic (+434/+8) | yeeW/yoeD | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related/pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2600973 | 38 (1.140) | 6 (0.190) | 6/246 | 2.9 | 14.1% | intergenic (+25/‑228) | bcp/hyfA | peroxiredoxin; thiol peroxidase, thioredoxin‑dependent/hydrogenase 4, 4Fe‑4S subunit |
| ? | NC_000913 | = 2600983 | 37 (1.180) | intergenic (+35/‑218) | bcp/hyfA | peroxiredoxin; thiol peroxidase, thioredoxin‑dependent/hydrogenase 4, 4Fe‑4S subunit | |||||
| * | ? | NC_000913 | = 2691168 | 35 (1.050) | 5 (0.170) | 5/236 | 3.1 | 13.6% | noncoding (173/184 nt) | glmY | sRNA activator of glmS mRNA, glmZ processing antagonist |
| ? | NC_000913 | = 2691173 | 32 (1.060) | noncoding (168/184 nt) | glmY | sRNA activator of glmS mRNA, glmZ processing antagonist | |||||
| * | ? | NC_000913 | = 3852844 | 38 (1.140) | 5 (0.160) | 5/238 | 3.2 | 12.2% | intergenic (‑60/+46) | ilvB/ivbL | acetolactate synthase 2 large subunit/ilvB operon leader peptide |
| ? | NC_000913 | = 3852855 | 37 (1.220) | intergenic (‑71/+35) | ilvB/ivbL | acetolactate synthase 2 large subunit/ilvB operon leader peptide | |||||
| * | ? | NC_000913 | 2543915 = | 52 (1.560) | 5 (0.160) | 5/244 | 3.2 | 10.2% | coding (709/792 nt) | ucpA | furfural resistance protein, putative short‑chain oxidoreductase |
| ? | NC_000913 | 2543976 = | 39 (1.250) | coding (648/792 nt) | ucpA | furfural resistance protein, putative short‑chain oxidoreductase | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 5 (0.160) | 5/242 | 3.2 | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 4530003 = | 42 (1.260) | 5 (0.160) | 5/250 | 3.3 | 11.7% | coding (241/1314 nt) | sgcC | putative PTS system EIIC permease component |
| ? | NC_000913 | 4530040 = | 35 (1.090) | coding (204/1314 nt) | sgcC | putative PTS system EIIC permease component | |||||
| * | ? | NC_000913 | = 3094073 | NA (NA) | 6 (0.190) | 5/246 | 3.3 | NA | noncoding (108/125 nt) | REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | = 3094083 | NA (NA) | noncoding (118/125 nt) | REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP216 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | 233792 = | 42 (1.260) | 5 (0.150) | 5/254 | 3.3 | 10.8% | coding (164/1359 nt) | mltD | putative membrane‑bound lytic murein transglycosylase D |
| ? | NC_000913 | 233828 = | 42 (1.290) | coding (128/1359 nt) | mltD | putative membrane‑bound lytic murein transglycosylase D | |||||
| * | ? | NC_000913 | 743425 = | 32 (0.960) | 4 (0.130) | 4/238 | 3.5 | 10.3% | coding (599/744 nt) | ybgI | NIF3 family metal‑binding protein |
| ? | NC_000913 | 743523 = | 40 (1.310) | coding (697/744 nt) | ybgI | NIF3 family metal‑binding protein | |||||