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 | 718,125 | T→C | Y78C (TAT→TGT) | yerD ← | putative osmotic shock glutamate synthase subunit (flavoprotein subunit, ferredoxin‑dependent) |
| RA | BS168_reference_genome | 892,022 | A→T | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 944,586 | T→C | S34P (TCT→CCT) | perR → | transcriptional regulator (Fur family) |
| RA | BS168_reference_genome | 1,073,527 | G→C | S64C (TCT→TGT) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| 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 | 2,387,885 | (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 | 3,059,489 | (C)8→7 | intergenic (‑88/+58) | ytnP ← / ← trmB | putative quorum‑quenching lactonase/tRNA (guanine‑N(7)‑)‑methyltransferase |
| RA | BS168_reference_genome | 3,474,002 | A→G | I211V (ATC→GTC) | yvbI → | conserved protein of unknown function |
| 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 |
| RA | Exported | 1,922 | C→T | intergenic (–/‑1056) | – / → eryR | –//vntifkey=4 |
| 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 | 160947–164866 | 165727 | 862–4781 | 23 [21] | [19] 23 | [rrnI‑16S]–rrnI‑5S | [rrnI‑16S],rrnI‑23S,rrnI‑5S |
| * | * | ÷ | BS168_reference_genome | 166435–166813 | 176228–172533 | 5721–9794 | 23 [21] | [21] 23 | rrnH‑16S–[rrnG‑5S] | rrnH‑16S,rrnH‑23S,rrnH‑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 | 201266 = | 93 (1.000) | 1461 (1.170) +57 bp |
102/138 | 0.0 | 60.0% | coding (990/1803 nt) | glmS | L‑glutamine‑D‑fructose‑6‑phosphate amidotransferase |
| ? | Exported | = 5904 | 3494 (0.780) | coding (17/324 nt) | lacZalpha | /vntifkey=4 | |||||
| * | ? | BS168_reference_genome | = 203026 | 92 (0.990) | 1143 (0.870) +53 bp |
98/146 | 0.0 | 55.8% | coding (433/912 nt) | alkA | DNA‑3‑methyladenine glycosylase; prophage 1 region |
| ? | Exported | 5962 = | 3058 (0.680) | coding (75/324 nt) | lacZalpha | /vntifkey=4 | |||||
| * | ? | BS168_reference_genome | = 640254 | NA (NA) | 114 (1.850) +42 bp |
45/168 | 0.0 | 65.9% | noncoding (117/117 nt) | rrnE‑5S | ribosomal RNA‑5S |
| ? | BS168_reference_genome | 951580 = | 89 (0.960) | intergenic (+8/‑2) | rrnD‑5S/asnTA | ribosomal RNA‑5S/tRNA‑Asn | |||||
| * | ? | Exported | 3854 = | 153 (0.030) | 2107 (0.470) +A |
167/250 | 0.8 | 96.5% | intergenic (+139/‑17) | eryR/ampR | /vntifkey=4//vntifkey=4 |
| ? | Exported | = 6538 | 0 (0.000) | intergenic (+327/–) | lacZalpha/– | /vntifkey=4/– | |||||