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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | BS168_reference_genome | 143,659 | C→T | S100F (TCT→TTT) | rpsE → | ribosomal protein S5 |
| RA | BS168_reference_genome | 165,749 | Δ1 bp | intergenic (+42/‑5) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,751 | Δ1 bp | intergenic (+44/‑3) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,826 | +C | intergenic (+1/‑4) | trnI‑Asn → / → trnI‑Thr | tRNA‑Asn/tRNA‑Thr |
| RA | BS168_reference_genome | 166,037 | +T | intergenic (+4/‑27) | trnI‑Gly → / → trnI‑Arg | tRNA‑Gly/tRNA‑Arg |
| RA | BS168_reference_genome | 166,345 | Δ1 bp | intergenic (+17/‑155) | trnI‑Ala → / → rrnH‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| RA | BS168_reference_genome | 376,025 | (G)8→7 | intergenic (‑227/‑7) | hxlA ← / → hxlR | 3‑hexulose‑6‑phosphate synthase (HPS)/positive regulator of hxlAB expression (formaldehyde sensing) |
| RA | BS168_reference_genome | 557,870 | (T)5→6 | intergenic (+421/‑3) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | BS168_reference_genome | 892,022 | A→T | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 961,037 | (A)5→6 | intergenic (‑51/‑357) | katA ← / → ssuB | vegetative catalase 1/aliphatic sulfonate ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,073,040 | C→T | A91A (GCC→GCT) | yhaI → | conserved protein of unknown function |
| RA | BS168_reference_genome | 1,073,489 | C→T | A77T (GCA→ACA) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,074,835 | C→T | G110G (GGG→GGA) | trpP ← | tryptophan transporter or sensor |
| RA | BS168_reference_genome | 1,317,152 | +GT | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,158 | (T)5→6 | coding (257/258 nt) | yjpA ← | putative enzyme |
| RA | BS168_reference_genome | 1,474,890 | C→T | L45L (TTG→TTA) | kre ← | regulator of transcription factor ComK function via modulation of mRNA stability |
| RA | BS168_reference_genome | 1,690,758 | C→A | R214S (CGT→AGT) | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 2,097,087 | (A)7→8 | intergenic (‑111/+39) | azoJ ← / ← yocK | FMN‑dependent NADH‑azoreductase/putative general stress protein |
| RA | BS168_reference_genome | 2,271,424 | T→C | R78R (AGA→AGG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,505 | C→T | V51V (GTG→GTA) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,523 | A→C | D45E (GAT→GAG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,308,413 | A→G | intergenic (‑74/‑82) | degR ← / → ypzA | activator of degradative enzymes (aprE, nprE, sacB) production or activity/putative spore coat protein |
| RA | BS168_reference_genome | 2,387,885 | (A)7→8 | coding (704/735 nt) | yphF ← | putative lipoprotein of unknown function |
| RA | BS168_reference_genome | 2,480,646 | 2 bp→AT | intergenic (+21/+103) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,480,654 | Δ1 bp | intergenic (+29/+96) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,480,667 | Δ1 bp | intergenic (+42/+83) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,581,732 | (T)6→7 | intergenic (‑115/+39) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | BS168_reference_genome | 2,626,240 | T→C | M570V (ATG→GTG) | dnaK ← | molecular chaperone, ATP‑dependent |
| RA | BS168_reference_genome | 2,633,093 | C→T | G43E (GGG→GAG) | yqxA ← | conserved protein of unknown function |
| RA | BS168_reference_genome | 2,770,869 | C→T | R174C (CGT→TGT) | rsiV → | anti‑sigma(V) factor |
| RA | BS168_reference_genome | 2,775,128 | T→C | R643G (AGG→GGG) | cypB ← | cytochrome P450 CYP102A3 |
| RA | BS168_reference_genome | 3,770,066 | (A)8→9 | intergenic (‑258/+38) | ywzF ← / ← csbD | conserved protein of unknown function/stress response protein |
| RA | BS168_reference_genome | 3,935,825 | Δ1 bp | coding (1190/1191 nt) | rlmI ← | large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | BS168_reference_genome | 4,153,115 | G→T | L192I (CTT→ATT) | walK ← | two‑component sensor histidine kinase [YycG] |
| RA | BS168_reference_genome | 4,155,395 | (A)5→6 | intergenic (‑186/+38) | trnY‑Lys ← / ← purA | tRNA‑Lys/adenylosuccinate synthetase |
| MC JC | Exported | 2,655 | Δ3 bp | intergenic (–/‑321) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 3,843 | Δ5 bp | intergenic (+128/‑24) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 5,049 | C→T | intergenic (+318/‑839) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160959–161238 | 165598–161240 | 3–4640 | 35 [33] | [24] 37 | [rrnI‑16S]–[rrnI‑5S] | [rrnI‑16S],rrnI‑23S,[rrnI‑5S] |
| * | * | ÷ | BS168_reference_genome | 166437–166812 | 171224–170066 | 3255–4788 | 34 [31] | [28] 34 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171465–171679 | 176234–172533 | 855–4770 | 37 [30] | [33] 36 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 3484069 = | 163 (1.250) | 23 (0.310) +34 bp |
17/184 | 1.1 | 25.2% | intergenic (‑295/+3) | cggR/araE | transcriptional regulator of gapA/arabinose‑related compounds permease |
| ? | Exported | 6207 = | 25 (0.350) | coding (320/324 nt) | lacZalpha | /vntifkey=4 | |||||