mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
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 | 1,211,308 | G→T | intergenic (+129/‑105) | mcrA → / → icdC | putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein/pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion |
| 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 | 2,661,793 | C→A | L113F (TTG→TTT) | iscR ← | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor |
| RA | 2,799,867 | C→A | R43L (CGA→CTA) | ygaC ← | uncharacterized protein |
| RA | 2,804,946 | +T | coding (132/1203 nt) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| MC JC | 2,904,286 | Δ122 bp | intergenic (+912/+340) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| 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 | 3,816,611 | C→A | intergenic (‑62/‑65) | rph ← / → yicC | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH/UPF0701 family protein |
| RA | 3,823,025 | G→A | R209H (CGT→CAT) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 4,178,239 | G→T | G166V (GGT→GTT) | nusG → | transcription termination factor |
| RA | 4,257,602 | A→T | N163I (AAT→ATT) | lexA → | transcriptional repressor of SOS regulon |
| RA | 4,267,824 | A→C | L237F (TTA→TTC) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423729–3424234 | 3424572–3424238 | 5–844 | 40 [37] | [39] 40 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 9 (0.120) | 61 (0.890) | 52/266 | 0.5 | 86.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 11 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.120) | 58 (0.840) | 47/266 | 0.8 | 85.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 11 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 82 (1.100) | 68/290 | 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 | |||||