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 | 197,804 | C→G | P260A (CCC→GCC) | cdaR → | regulator of diadenylate cyclase activity |
| RA | BS168_reference_genome | 333,932 | G→A | L16L (CTC→CTT) | mdr ← | multidrug‑efflux transporter |
| 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 | 1,073,374 | C→T | W115* (TGG→TAG) | 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→G | R214G (CGT→GGT) | 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 | 2,134,705 | T→C | Y228C (TAT→TGT) | ldcB ← | D‑alanyl‑D‑alanine carboxypeptidase lipoprotein (D‑ala releasing from tetrapeptide hydrolysis) |
| 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 | 2,485,359 | T→C | F150S (TTC→TCC) | yqjF → | conserved protein of unknown function |
| 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 | 2,778,062 | C→T | D120N (GAT→AAT) | yrhH ← | putative methyltransferase |
| RA | BS168_reference_genome | 3,373,796 | T→A | D18E (GAT→GAA) | yuzM → | 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 | pSIJ663_pHT315_araE_xy | 2,186 | (T)8→7 | intergenic (–/‑792) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 2,655 | Δ3 bp | intergenic (–/‑321) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 3,843 | Δ5 bp | intergenic (+128/‑24) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,049 | C→T | intergenic (+318/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160964–161238 | 165603–164903 | 3666–4640 | 20 [14] | [15] 16 | [rrnI‑16S]–[rrnI‑5S] | [rrnI‑16S],rrnI‑23S,[rrnI‑5S] |
| * | * | ÷ | BS168_reference_genome | 166442–166702 | 171217–170391 | 3690–4776 | 17 [13] | [14] 17 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171467–171676 | 176206–172533 | 858–4740 | 19 [15] | [12] 16 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| * | * | ÷ | BS168_reference_genome | 202117 | 202131 | 15 | 22 [15] | [15] 17 | [ybbU] | [ybbU] |
| * | * | ÷ | BS168_reference_genome | 3485340–3485462 | 3486758 | 1297–1419 | 16 [15] | [0] 50 | [araE]–[araR] | [araE],[araR] |
| * | * | ÷ | pSIJ663_pHT315_araE_xy | 5552 | 11152–9809 | 4258–5601 | 4340 [34] | [2419] 2437 | ampR/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 390841 = | 89 (1.180) | 79 (1.050) | 46/254 | 0.2 | 51.0% | coding (3098/10752 nt) | srfAB | surfactin synthetase |
| ? | BS168_reference_genome | = 1117696 | 63 (0.830) | intergenic (+9/+38) | comK/yhxD | competence transcription factor (CTF)/putative oxidoreductase | |||||
| * | ? | BS168_reference_genome | = 449683 | 94 (1.240) | 72 (0.990) | 34/244 | 0.5 | 51.0% | intergenic (+132/‑41) | ycnL/mtlA | putative reductase or disulfide isomerase/phosphotransferase system (PTS) mannitol‑specific enzyme IICB component |
| ? | BS168_reference_genome | 1117084 = | 48 (0.660) | intergenic (‑268/‑25) | yhzC/comK | conserved protein of unknown function/competence transcription factor (CTF) | |||||
| * | ? | BS168_reference_genome | 3486759 = | 0 (0.000) | 22 (0.020) +50 bp |
16/154 | 0.9 | 94.8% | intergenic (+1/+48) | araR/yvbT | transcriptional repressor of the ara regulon (LacI family)/putative alkanal monooxygenase |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | 4 (0.000) | intergenic (+5050/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5551 | 34 (0.010) | 4190 (1.130) | 186/244 | 0.0 | 99.2% | intergenic (+820/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9889 = | NA (NA) | intergenic (+5158/–) | ampR/– | –/– | |||||